Why does nitration of aromatic amines give meta directed nitro compounds? Amines are activating groups and donate electrons to the resonance structure using the lone pair of electrons on Nitrogen.
But when aromatic amines are nitrated, for example when benzyl amine is nitrated, it gives a meta nitro benzyl amine.
Given the activating nature of amine groups, shouldn't the compound be an ortho-para directing variant?
I tried figuring it out. One explanation I've come up with is that when it's nitrated, the proton from the nitrous acid forms a coordinate covalent bond with the amine group closing the lone pair electron to the bond. As a result it becomes an $\ce{NH3+}$ group. That would mean that it has a deactivating effect or electron withdrawing effect. That's why the incoming nitro groups are attached to the meta positions. But then why doesn't the same happen for nitration of hydroxide groups, for instance phenol?
A couple things here.  First, it's nitric acid, not nitrous acid, that is the nitrating reagent.  Otherwise, your own explanation is correct.  Orthocresol points out that phenols are sufficiently inert to protons, to avoid this situation.

Second, you can make ortho/para directed nitrated aromatic amines, if you are a little more clever and if you have a tertiary amine (http://www.chem.ucalgary.ca/courses/351/Carey5th/Ch22/ch22-3-6.html).  Use nitrous (not nitric) acid, which is weaker and will react only with the unprotonated amine.  That gives you a nitroso $\ce {-NO}$ group which you can then oxidize to the nitro group.