Are websites protected by the US Constitution?

I'm a super moderator on a forums (Gamelair) and a devout atheist. I have made a thread that discusses religion and science, and argues each side's view. It has been going for a few months now, and is one of the oldest popular threads. Recently the issue has come up if the thread is protected by the US Constitution (For freedom of religion, Amendment 1. Some members are complaining about the thread, and saying that it needs to be closed down. However, NO rules have been broken in the thread.) since Gamelair is based in the US. I think that bloggers aren't protected, but what about forums?