Definitely - and I've moaned about it in my LJ, but haven't provided all the details. My main character is in a very abusive situation (similar to a bad marraige, except she's been kidnapped) and writing it is emotionally draining - but it's stuff that I know, and I know the writing is good, because I can to some extent understand this subject. If it wasn't for that, I don't know if I could keep going, and even as it is, I'm writing for YA and I don't like all the disturbing stuff - and the swearing - that is happening.
As you write, you may find depths of understanding you didn't know you had, but it's never easy. Rest assured - it's quite normal for authors to cry over their writing (not because it's bad, I mean, because they get too involved with what's happening to the characters.)
Good luck!