The problem with this argument is that people simply don't understand the effects of scale. Religious individuals may be very reasonable people for the most part but that small amount of "don't question, just accept" has a huge knock-on effect when multiplied by billions.
Religion is the basis of the decay of independent thinking and that affects everyone in society, including atheists. While we may not believe in gods and miracles, many atheists still believe that the almighty politicians and corporate "job creators" are looking after us from their aristocratic heaven. Those who don't want to take part in this modern day religion are forced into submission through social pressure.
As atheists and pioneers of free thinking it is our responsibility to make it clear that irrational beliefs are hugely detrimental to human society. It is not acceptable for people to nurture mindless obedience anymore. We are all forced into slavery by the submission of our peers.