Several groups have filed a lawsuit to exclude "so help me God" from the end of the president's oath. I whole-heartedly agree that there should be no requisite references to any particular religion/deity in government proceedings. However, I also am glad to see that this lawsuit does not include the president-elect himself, because, "...he possesses rights as an individual that allow him to express religious beliefs."
I think that is the fundamental difference that many people get upset over; Efforts to prevent religion from being taught in public science classrooms, or to exclude any reference to a deity from the pledge to our great country are not intended to silence anyone's personal views. In fact, they are intended to to the opposite - to welcome and be inclusive of the multitude of cultures and beliefs that co-exist somewhat peacefully here.