Many people argue that atheists pick on all theists when the fundamentalist/extremist ones are mostly at fault and the majority of theists are more benign and beneficial to society.

This is wrong. ALL theists and ALL forms of theism are harmful and destructive. The points outlined above are not specific to fundamentalist extremists; They are common among virtually all theistic denominations.
Contrary to what most may believe, moderate theists are the most destructive. This is because they provide the cover (as well as the breeding ground) for the fundamentalists. They are the major force that will not allow open and honest debate on theism to exist in the public mainstream media. There are many great documentaries on science and theology that will never air in the United States because theists, even moderate and liberal ones, would not tolerate such discussion. This is because theism really doesn’t have much of a legitimate, rational leg to stand on. The very fact that theists would rather not have their beliefs critiqued further underlines the reality that their beliefs are most likely not rational and that theists are most likely unable to defend them in an open forum.
For this reason, Atheists cannot pick and choose certain factions of fundamentalists to rail against. In truth, all theists — from extremists to liberals — are part of the same deluded group. They all create the same problems for our society, and it would be intellectually dishonest to claim otherwise.
Sam Harris gives another great presentation on this issue, going beyond the basics to explain why even moderate and liberal theists should be considered a threat to freedom, science, rationality and peace:

