Is it that 'new atheists' like Sam Harris simply don't understand religion (beyond assembling everything bad they know to attack it with), or is the failure to distinguish positive and negative deliberate?

That's one question that occurs when reading their books and articles.

Ali Eteraz is an astute commentator on Islam and tackles one kind of misrepresentation perpetrated by best-selling author Sam Harris:

In many ways, Harris makes the same mistake the fundamentalist Muslims do, which is to believe that self-critical Muslims are not as sincere about their faith as the fundamentalists and therefore they do not represent the "real" religion. This is the basic fallacy that prevents him from realising that the Islam that self-critical Muslims adhere to is, at the end of the day, Islam.

Full article: http://commentisfree.guardian.co.uk/ali_eteraz/2008/05/islam_isnt_islami... [1]

See also, 'True faith is always asking questions' - http://www.ekklesia.co.uk/node/7034 [2]