To me, and I'm entitled to my own feeling about "E Pur Si Muove" ;), it also stands for a strong believe in one's own observations, a strong will that is not swayed by the masses and the loneliness that comes with it. The sentence "E Pur Si Muove" may provide people with the strength needed to voice their unconventional theories.
It means that the material world is what it is, and that reality is not modulated by human decree.