Protected classes were defined in the law only because we decided they should be. Nothing says it can't include more or fewer things as the winds of opinion blow in a different direction. A religion isn't really much different from other belief systems after all.
This is a common error in reasoning by the way: looking to the way current law happens to be and inferring from that what the right thing to do is. For example, it is not against the first amendment for Amazon to ban Republicans. This does not mean it would be a good thing for Amazon to ban Republicans. Similarly I'm sure, if you tried, you could come up with all kinds of unjust laws that punish things that should not be punished (I certainly can think of many).
This is a common error in reasoning by the way: looking to the way current law happens to be and inferring from that what the right thing to do is. For example, it is not against the first amendment for Amazon to ban Republicans. This does not mean it would be a good thing for Amazon to ban Republicans. Similarly I'm sure, if you tried, you could come up with all kinds of unjust laws that punish things that should not be punished (I certainly can think of many).