I in no way intend to speak for anyone here (they can speak for themselves) but many atheists (and some agnostics) are anti-Semitic partly because the Jews believe in God, nay they KNOW there is a God. They even have EVIDENCE that there is a God. To the atheist who thinks the evidence shows there IS NO God, this stance of the Jews is evidence of their mental inferiority to "intelligent (read: 'atheistic') people". And the Jews' insistence that there is a God who wants us to act in certain ways, while avoiding other actions, may be seen as a plot for world domination, Jews on top, everybody else on the bottom, because the Jews claim to know what these actions are. Thus, to this type of atheist, they (the Jews) need to be eradicated.
"The enemy of my enemy is an ally", so these kinds of atheists support terrorism against Jews, world-wide.