I believe the fines do go to charity. There is a clause in all contracts requiring players to "make themselves available to the media", whether they like it or not, it's what they sign up for...
Found a link regarding charity:
http://mentalfloss.com/article/53212/where-does-nfl-fine-money-go
I also found this quote, which I like:
Mike Sando, ESPN.com: “Professional courtesy seems like a reasonable expectation for all involved. The NFL’s media policy works well most of the time, but no one can force compliance. If a reporter violates the policy, he or she can lose his or her credential. If a player or coach violates the policy, he can be fined. That seems reasonable and fair.”