We Americans assumed that 9/11 was "all about us"; hence, "they hate us for our freedom". At the foundation, I think that it simply is that the West, as a whole, is not officially Muslim, under Sharia Law, and so must be forced by any means to submit to Islam. They hate us because of who and what they are.
Theists, and others, feel -- it's a matter of mass psychology -- that what their group preaches and parrots is what makes reality, and not only their reality but reality for everyone. Football fans, en mass, create a reality of which each fan is a part; it is the experience of the mass event as much as it is the game per se. The Jehovah's Witnesses feel that the more time, energy, hope, and hours going door-to-door that they put out, the sooner "Jehovah's Kingdom" will come. Theists "go to church" to generate and reinforce their "reality". Theists send "missionaries", a high status designation. The more visible and in-your-face that atheists become, the more the theists' hard-won "reality" shakes and shimmys, and the more faint their hope of "heaven".Remove a theist from their reinforcing milieu, and watch them fall apart; I do not think that is the same for atheists.