Yes, every study has limitations. The fact that you can't do a blind study or a placebo control with circumcision is just a fact of life -- people tend to know if they're circumcised or not. This does not refute the many studies' findings.
Can you imagine the outrage if the author published a paper questioning the effect of smoking on lung cancer, and then wondered if smoking actually reduces your chances for lung cancer? That's what this article is doing.
I'm glad that Gates is standing on the side of science here.
1. http://www.croiconference.org/sessions/impact-male-circumcis...