The answer is simple.
You just need to think about how you learned your native language.
By ear.
Children learn how to speak their native tongue first, and only then learned the grammar and spelling.
Thus, many will "sound" a word out to spell it.
English language learners, on the other hand, usually learned how to spell a word first, and focused on pronunciation later.
english.stackexchange.com/users/134/OneProton
I think that the same goes for all languages.
Native speakers that do not take the time to learn their own language properly, or that do not read much, tend to misspell homophones.
In French, for instance, many people will replace infinitive form (« manger », to eat ) with past participle (« mangé », eaten ), or confuse « ses » and « ces
» (his,her vs these).
Astonishingly enough, foreigners that study the language do not have this homophony problem in their “source language” and therefore are aware of a grammatical difference.
It sounds like people assume translation is mathematically speaking an injective thing.
english.stackexchange.com/users/1487/Benoit
The confusion is that in many UK (and probably US) schools the difference is not taught.
The use of the apostrophe is considered by many to be totally confusing and so it is omitted in many places where it is required.
There is a name for the addition of extra apostrophes in places where they are not needed.
These are "Grocers' Apostrophes" which refers to the common sight on market stalls and grocers' shops where the price labels may erroneously refer to "Banana's" or Apple's".
english.stackexchange.com/users/1578/uɐɪ
Sometimes I wonder how often this mistake is made out of carelessness, versus ignorance.
I'm well-versed in the difference
betweent the two, yet
I've still made the gaffe on occasion.
Due to the homophoneous nature of the words, the mistake is easily made while typing, and particularly easy to miss while proofreading, too.
english.stackexchange.com/users/18220/J.R.
In American English (I can't speak for other varieties), even though the two are both spelled and pronounced distinctly in standard writing and slower articulate speech respectively, they tend to be pronounced the same in regular speech.
you're =
\yər, ˈyu̇r, ˈyȯr, ˌyü-ər\ and your = \yər, ˈyu̇r, ˈyȯr\ (from Merriam-Webster, with American rhotic pronunciation).
Note that the only difference is the one variant for "you're".
So it is understandable that there is the possibility of mistaking one for the other.
This pair, like other homophones are often mentioned explicitly in language studies in elementary school in the US.
Making the mistake later in life is usually simply a one time mistake (like the other homophones).
If the mistake is systematic then that is probably a sign of lack of concern for orthography.
english.stackexchange.com/users/4972/Mitch
I think people get confused because the apostrophe is used in possessives as well as contractions, but in this case the possessive
your has no apostrophe.
english.stackexchange.com/users/720/kajaco
Not an answer as such, but I'm sure this might help some people: http://yourandyoure.com/ :)
english.stackexchange.com/users/984/kguest
I have seen many comments on different blogs and forums where English native speakers spelled  you're  as  your . I'm not a native speaker, but I know and understand the difference between the two. Why is there a confusion?  My initial guess is that  your  and  you're  have similar pronunciation and because I carry some accent from my native language (Romanian) I can identify the difference better.  Edit  (thanks Chris): The same can be asked for other homophones:  there/their/they're ,  its/it's .
"Your" vs. "you're": Why the confusion?
english.stackexchange.com
<possessives><contractions><pronunciation-vs-spelling><homophones>
english.stackexchange.com/questions/3738
english.stackexchange.com/users/1580/Alexandru
Thes two words tend to be pronounced the same in regular speak and it's possible that in many UK and US schools, the difference is not taught. Furthermore, native speakers are naturally more susceptible to making spelling errors with homophones. It is believed that the confusion arises because the spoken language is generally learnt first then the spelling, but for English speakers, they learn the spelling first and then the pronunciation. However, some believe that the spelling comes first and then the pronunciation afterwards, which is the cause of the confustion. Equally, native English speakers do not learn their language correctly and confuse homophones; words spelt and pronounced the same. Some believe this homophonic difference is not properly tuatht in schools, although others suggest it is explicitly outlined in elementary schools in the USA. Some people believe that the presence of the apostrophe, also known as the Grocer's apostrophe can cause confusion because it is also used in contraction and possessive forms. It is considered that the mistake is either carelessness or just poor attention to orthography.
Thes two words tend to be pronounced the same in regular speak and it's possible that in many UK and US schools, the difference is not taught. Furthermore, native speakers are naturally more susceptible to making spelling errors with homophones. Sometimes this mistake is made due to carelessness and sometimes due to ignorance.  Even though the two are both spelled and pronounced distinctly in standard writing and slower articulate speech respectively, they tend to be pronounced the same in regular speech.   Due to the homophoneous nature of the words, the mistake is easily made while typing, and particularly easy to miss while proofreading, too. Native speakers that do not take the time to learn their own language properly, or that do not read much, tend to misspell homophones.  
Native speakers that have not learned their own language properly, or that do not read much, tend to misspell homophones.   There is regular confusion with these two words because they are pronounced the same in regular speech. Furthermore, the difference may not be taught very well in English-speaking countries and native speakers a naturally more susceptible to making spelling errors with homophones.
The confusion is that in many UK (and probably US) schools the difference is not taught. The difference is not often taught.
You learn the correct spelling from the pronunciation.  Native speakers do not learn their own language correctly, read very little and so mispell homophones. This is not the case for foreign learners of English.  The confusion arises because the difference is not taught.  Although some say the difference is taught .  The placement of the apostrophe is often incorrect.  The confusion is due to carelessness rather than ignorance. However, sometimes the mistake can be just a once off or indeed it can be careless orthography.
Native speakers that do not take the time to learn their own language properly, or that do not read much, tend to misspell homophones.   Sometimes this mistake is made due to carelessness and sometimes due to ignorance.   Due to the homophoneous nature of the words, the mistake is easily made while typing, and particularly easy to miss while proofreading, too. Even though the two are both spelled and pronounced distinctly in standard writing and slower articulate speech respectively, they tend to be pronounced the same in regular speech.   
Native speakers in general are more likely to misspell homophones. It could be that the difference between these two words is not taught very well in English-speaking countries. Although both are written differently, they are pronounced the same in regular speech.