Atwood admits that your, "essay does contain some fair points," but he also indicates that he, along with others, had trouble getting through it because of the distasteful metaphor you lead with. In light of this, I am sure you can understand them not spotting the thesis in your last paragraph.
Finally, perhaps someone with a "conscientiously broadened mind," as you so describe yourself, could fathom a working environment unlike the one you describe? I imagine that new-hires at 37signals, or Fog Creek, would not feel they are missing out because they are not currently heading a start-up. Quite the opposite, I would think they are grateful for the opportunity, the environment and the benefits. Not all successful companies treat their developers like animals. And the ones that don't tend to inspire loyalty. Can you really not see how you may have offended some of these people?