I booked my room through the portal.  Everything I read says that I will be charged $50 for cancelling my room.  Still?  Really?  

 As of your posting, neither the city of Indianapolis nor the state of Indiana have required the cancellation of the Gencon.  That means as of now standard cancellation rules are still in effect.  If they are required to cancel then I would imagine that cancellation rules will be changed.

So who do I need to talk to about the $50 cancellation fee?  Gencon on the hotel I booked through?

Your hotel will not have your reservation until a week or so before the convention, it's currently being held with Q-Rooms. You'd probably need to take it up with Gen Con. 

of course if you just wait, if/when gencon is cancelled all the reservations will be cancelled and should be with no penalty.  

Yea looks like if I cancel anytime between now and June 6th, it's $50.  So my plan is to wait until June 5th and cancel then if there hasn't been an official announcement.  I'm not worrying about my badge, but after dropping $135 on a  badge, I'd at least like to avoid a $50 hit on top of that.    

You should wait until it's dates are changed or it's cancelled(if). Im sure they will drop most penalties 

No reason not to wait. June 6th is still some 6 weeks away...

I would be stunned if no announcement is made by then.

G
 

My only piece of advice would be: if you know you for sure are not going, even if the event isn't cancelled, modify your reservation to one further away, so that the people that still plan to go cantry to get a better room.