So after a few months of riding the F Train late at night I'm happy to report that it's a very safe ride. I never had problems even early in the AM, drunk and half asleep.
It's not like the train's packed (especially in queens) but there are a few people who ride to the last stop and the 179th st station doesn't strike me as particularly scary. I've felt more unsafe at certain manhattan or brooklyn stations late at night.
My feeling is that as long as you're minding your own business you're fine. Then again, crazy people can bother you on any train at any hour of the day, ans muggers can wait for you everywhere. So I guess you can never be sure. But as long as the F Train goes, I don't see where the problem is. And as someone wrote a few pages back, there are no crazy people on the train until manhattan