The 'Heil', most famous for it's association with Adolf Hitler and the Nazi party in WWII Germany. This doesn't hurt anyone either, it's just holding your arm out straight with a serious look on your face. This doesn't effect anyone else, so what's the problem with it?
The problem with it is it supports a man, and an ideology which was deemed highly immoral, as indeed it was. It shows support for what he was doing. It supports the ideals it was founded around.
This is why some Atheists oppose praying. It supports the ideology of religion, which most Atheists hold in contempt. Ignoring the fact that it's illogical and completely useless, it shows that you subscribe to, and support the ideology it is based around, religion. Religion is the true organisation many active Atheists oppose, as they should (RE:Why Atheism Is So Important). For me at least, this is one of the reasons I oppose praying.
An important thing to note though is that I don't think prayer should be outlawed for individuals to practice in their own home or in public. It should be kept out of schools, in alignment with the separation of church and state, which is outlined in the constitution. But it should be free for individuals to practice whenever they want. I just think those individuals should be laughed at and ridiculed by the community when they do, in the same way big foot enthusiasts are ridiculed and laughed at.