Show the mom what you wrote here, and talk together to a family counselor. If something is going on, you need to learn it, but you also don't want to make false accusations. Any questioning of the child might be best done by the counselor after you three discuss the situation. (And should probably be filmed when she does talk to the child, so there will be no accusation later if charges are brought that the child was questioned in a way that coached her to say things that weren't true.) The reason for all this caution is that when there is suspicion that something has happened to a child, accusations can fly around that you are the molester from the person who is the molester, and/or assumptions can be made that aren't even true at all. Get the question of sexual abuse figured out right away.
Regarding the child being frightened of going to sleep alone, once you are sure the child is merely anxious in general and not being molested (and of course, that is the biggest thing to deal with), you and your wife should get the book "What to Do When You Dread Your Bed" by Dawn Huebner, and work through it with the child. (It's a workbook, you don't just read it to the kid and everything is magically OK.) It is very well done and I can tell you from experience that you don't want this bedtime-fear thing to be a continuing issue.
But again, since she could be the victim of the dad's roommate or someone else, you really need to sort this out first and take it very seriously.
Good luck, I'm sorry this has fallen on your plate and sorry if it is true. What you can do for this child is model that not all men are bad. If she is being molested, you can show that most men would find that an outrage and that you will fight to protect any child from any predatory adult.