I have a infant son who lives with his mother, we're not married. He is 5 weeks old and came over with a big red mark on the back of his head.
I asked the mother and she said "she had seen it" 12 days later he got to go to the doctor after CPS came out to investigate and saw his head.
He now has 3 doctor appointments to go to for his head and CPS said "I had to give him back to the mother." Come to find out she never even took him to the doctor to get his head checked out. I want my son to be safe, what can I do to help him? Can I get temporary or full custody of him?
What is a father to do?

First being married or not being married has little to do with it.

Next are you on the birth certificate, that is important.
Next have you filed in court for partial, joint custody or visits.

You have rights to custody even without CPS but that will help you get it.

Since you mentioned Florida are you registered with the state yet ?

Putative Father Claim, Search and Update Information and Applications (http://www.doh.state.fl.us/planning_eval/vital_statistics/Putative.htm)

Yes I am on the birth certificate, but I haven't filed anything in court. Could I file for emergency custody? Or do they have that?

What do you mean by registered with the state, like to live here or voting?

Check the link it explains it to you. It's a fathers registry that Florida has.