Question: When I activate BitLocker, I imagine that will make it impossible to read any files on my Windows partition from my Ubuntu installation. Is that correct? 

Any way to *not* encrypt certain directories so I can access them from Ubuntu?

Answer: 
Yes.

Bitlocker is whole drive (partition) encryption, it has its own bootloader from start to finish. It is the easiest solution for encryption.

You may even have a problem booting into Ubuntu all together if your machine has a TPM chip as Bitlocker ties in to that to check integrity.

Your best bet would to be have a partition used just for moving files in between the two systems.

You may also want to take a look at using [Truecrypt](https://i.stack.imgur.com/7vzXY.jpg) as this can achieve what you want very easily. Alternatively, if you want a Microsoft Solution, Microsoft have a option called [EFS (Encrypting File System)](http://en.wikipedia.org/wiki/Encrypting_File_System) that works very well and can do what you want, if not a little complicated to learn / get into.

AFAIK, EFS cannot be read from any NTFS compatible driver/app in Linux, where as you should have no problem using Truecrypt in a cross platform environment, so you could even encrypt everything and still open it up in Ubuntu.
Alternatively you might also try an encrypted EXT 3 filesystem that you can access from windows using FreeOTFE. I tried Truecrypt before, but especially in combination with SVN, which causes a lot of file accesses during an update, truecrypt was very slow.