In what sense is Doctorow himself causing the same sort of suffering against which he's inveighing? The parallel makes no sense.
Doctorow does not sell only on Amazon[0]. He also has a history of giving his books away for free[1], and insists on every release of his books in any format being DRM-free. Since those are the issues he is passionate about, that doesn't seem hypocritical to me.
It's more like PETA protesting in front of shops that sell furs, rather than only in places where people are already 100% anti-fur. Which... they probably do. Obviously.
The ultimate point of the book is to gather support for legislation that would give teeth to antitrust. It needs to reach sufficiently many people for that, and only the likes of Amazon can provide that kind of outreach. If it succeeds, the meager profits off the book that Amazon will skim in the process won't matter. Of course, whether it succeeds or not is a gamble, but it's a reasonable one.