However, what is the last refuge of a small, marginalized minority under tremendous external pressure (such as a real attack on their rights and/or rapid social/political/economic changes that result in great anxiety and fear) with limited political power? Terrorism. By the logic you've employed, Al Quaeda would pose no threat to us b/c they're not taking over a political party. Neither would the Christian Identity Movement b/c there are only 350,000 CIM members in America, Canada, and Great Britain combined, they are seriously marginalized, and they have no real political power.
Do I think "atheist extremists", or "antitheist extremists" if that works better for you, will necessarily become terrorists. No. But I also don't think we should allow tunnel vision to set in. Just b/c the enemy before us is great, doesn't mean there isn't an enemy sneaking up from behind. Remember: the religous right was once a marginalized minority within the right that the left refused to take seriously as a potential threat.
Sounds eerily Malkinish.