Flip this around. Let's say there's a restaurant that charges Christians more $$ for the same food dish than atheists. (And I agree with the argument that offering one group of people a discount and another group not is essentially the same thing as charing more for the same service to the latter group.) Anyone here want to guess how Christians would (as a whole) respond to this?
Here's betting that they'd react very similarly to how the atheists have acted here.
Yes, restaurants, stores, service providers offer senior citizen discounts, charge less for veterans or members of the military, etc., but not all group distinctions are equal. For better or worse, this country, and its legal system and traditions, treat religious discrimination differently than they treat these other forms of discrimination. Frankly, continuing to argue that these are all equivalent forms of discrimination really misses the mark--by a wide amount.