Sorry to hear about your FIL, I hope he is progressing.
Regarding the crying, it could be either physiological or psychological or both, it depends where the damage is in his brain. If this is the case time is required to heal & keep an eye open for related psychological events too.
Crying is extremely common amongst us Strokees. It not only occurs in depressed people but it can be an outlet for frustration, being overwhelmed, guilt, etc. These things may lead to depression but my point is you don't have to be depressed to cry.
Remember, your FIL has had a brain injury & the massive change that accompanies it. Recovery from stroke is slow, please don't apply your usual measures ("he should be better by now"), everyone is different but it is always slow. Be there to love & support him, get him the professional help he needs when he needs it.
After my stroke I cried over things and couldnt explain why I was crying. Maybe its just part of the recovery process. But I can certainly relate. Once I would go out in public, people at our bank scared me. They looked different to me, for some reason I can't explain. I would just start crying, and shaking..and they knew me by name, we live small town. I had my stroke on Oct 13,2008, and was 37 yrs old. I know the best thing that helped me was my family, very understanding and very patient.