I would argue that in this case, the discrimination cannot really be fought successfully.

See, most forms of discrimination can be fought through the help of "allies." The dominant group is going to hold power so long as the subordinate groups are fighting alone. For example, gay males are quite often allied with straight females, since women tend to simpathize with gay males, and they can use their "straightness" advantages to help aid the gay males in fighting the discrimination.

However, in the case of religion, the dominant group, the Christians, believe that they are right and everyone else is wrong. There are no Christians who are going to help atheists fight, and the atheists cannot fight alone due to the lack of power.

It all gets quite complicated and I think I'm having trouble explaining it accurately, but in this case it just doesn't look like there's much hope until Athiests become the majority rather than the minority.