I don't think your comment was designed to criticise Muslims, but I think you did a sloppy job making your point, and equivocated (maybe accidentally) the wrong sets and members.
Charitably, your comment reads that people who call themselves Nazis today are as far removed from (and do not bear the mantle of) the Nazis of WW2, as Muslims are removed from Islamist terrorists.
Again, charitably, that is an appalling comparison. Because it implies the reverse too; that Muslims are as responsible for the crimes of 9/11 as one believes modern Nazis are for bearing the history of the National Socialist movement - which of course they (modern Nazis) are.
More clearly: The perpetrators of 9/11 are only tangentially part of the same group as Muslims in general. You may as well group these NeoNazis with the set "Americans", or "White Men", as their motivations have as little bearing as regular Muslims and the men who brought down WTC.
As before, the better comparison is to ask if non-violent members of ISIS or Al Qaida can be assumed criminals/terrorists, as their violent companions are.