I don't see where there is any legal avenue for protest here - sure you can say you "don't like it" and that's your right, but it's also just your opinion, not backed by anything substantial. Is a group going to stop saying something because you don't like it, and is a company going to turn down money because you don't like it? Probably not. I've seen religious signs here, while I'm sure there are some secular protests against them, it is free speech and if they want to spend their money on doing that, well, that's their business.
While atheism and such aren't "religions" proper, but rather a movement against them or at least supporting the idea of no religion, if need be, atheists could easily organize and get official legal recognition as churches, if any sort of religious-only law or policies get enacted to try to block atheist groups from having the same rights as religious ones, because it isn't up to anyone else what constitutes a religion.