I concede that you raise some good points, but I still think this falls into the category of discrimination.
What if the newspaper/billboard regularly ran ads for catholic churches and synagogues but refused to run an ad for a mosque. Wouldn't that be a case of religious discrimination? Regardless, I don't think the comparisons are apt in any case, as in those examples the owner could turn down the sale to hate groups because their billboard/ newspaper would have their names attached to a property and it would hurt future sales.
The printers does not have that issue as the customer's own the shirts and the company's name is not associated with it. It could not hurt their sales.
As for the free speech side of the argument, I don't see it as them helping promote a message they oppose; but, rather as the printer denying service to someone because of their religious beliefs. Printing the shirts in no way means that they endorse the shirt. Its their customer's slogan, one which states only the customer's opinion upon the existence of god. It does not make disparaging remarks against theist, only states the opinion of the customer.
If the shirts said, "Gotta keep it real Like Bathsheba" or simply "Gotta keep it real like God" would the printer of turned them down? I don't know, but i have my doubts. If they would turn them down, then that would be fine as they are treating all religious beliefs equally. However, if they would print those but not this one, then they are singling out atheists. How is that not religious discrimination?
Further, what actually do they object too? Is it the part about god not being real? If so their objection is against atheism itself. The shirts say nothing against theists. Its like the florist example. Does a florist have the right to refuse service if their flowers are going to be used at a gay wedding?
I admit, in both cases it is a case with a fine line that our government needs to walk between free speech and the right to not be discriminated against.