As has been asserted in fragmented bits all over the place (here and in the original Google+ thread), the problem is that there is an enormous hiatus between personal and social ways of approaching gender.
On an individual scale you can see how personal expressions of sexual and gender identity can vary. [1] On a social scale, however, we deal with gender in a grossly simplified manner (and there are linguistic and historic forces which constrain us into defaulting to this attitude).
Mr Munroe is bringing up some issues (for what is worth, that of female-bullying attitude on the internet should be known to any gardener of virtual communities here on HN). But the whole issue is a much messier Pandora's box.
There are many people of either biological gender [2] who for different personal reasons wish to be more or less defined in terms of their sexual and gender identities, and in ways that a simple "I'm a {he, she, it}" form won't permit.
Imposing a (forcefully public!) choice is stepping on many people's toes, and I'm not quite sure what's the relevance of that. Google is smart. They could be gathering much better user-targeting data if they had implemented gender identity as a text field in the profile. [3] You know more about people (regardless of gender) who would fill that textbox with "dragon" than you can ever know about someone merely because they chose between man, woman, or other.
[1] An elegant if simplified reflection of what I'm talking about is given in this thread: http://news.ycombinator.com/item?id=2741580
[2] Not to mention the outliers to this binary opposition.
[3] See this thread: http://news.ycombinator.com/item?id=2741536
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ps. — EDITED a couple phrasings.
pps. — Concerning your EDIT #2, I see where you're coming from and I assume no bad faith from you, but please realise that this position you're assuming is very hard to tell apart from the "she was raped because she was dressing slutty" argument which set the internet afire not a couple months ago.