Not so much genius as just an absurdly hardcore work-ethic, and a refusal to ship code that is sloppy where it would matter.
Well the things he has worked on and pioneered arent a result of just hard work, as computer graphics is one of the most complex fields in our industry. There is no doubt that he is a super smart guy with an unparalleled work ethic.
This stands in stark contrast to the "other John" from iD (http://en.wikipedia.org/wiki/John_Romero) that went on to flame out in the most spectacular manner because he'd waffle between not shipping at all, or shipping half-baked games.
After reading that book I don't think there's any way you can come away without seeing him as one of the top 25 programmers in the world. Mad genius for sure.