IQ does not equal intelligence, except possibly in the extreme subsets of mental abilities which actually feature on the test. It's not been treated seriously in the scientific community for almost ever. It's almost solely a cargo cult for people who excel at it and want to feel superior.
The scientific debate is much more complex than you give it credit for. Yes, there really are people who believe that IQ, or (to be more sophisticated) g, really has validity. I personally view it as convenient shorthand, but not real. However this is not a universal position. For a take on why it is probably not valid, see http://cscs.umich.edu/~crshalizi/weblog/523.html.
But whether or not you accept that IQ is meaningful, the following fact remains true. On a wide variety of abilities that we can measure, including most specific mental attributes (working memory, processing speed, etc), males have much higher variability than females. The average gender differences are small, but men are over-represented in both tails. That fact is true both when abilities are measured in isolation, or on a test that aggregates them, like a standard IQ test.
Of course, it's not politically correct to say that there are more guy geniuses than girl geniuses, no matter how convincing the data may be. Saying that there are more male idiots is presumably perfectly okay; people who care about such things generally only care if it's the "minority" (never mind that women are a numerical majority in the US ).
Caveats: I don't know how convincing the data is. My point is that the discussion would not change even if the science happened to be completely airtight. Anecdotally, many of the intelligent people I've met over the years have happened to be women, so I'm inclined to believe in equality or even a female-favorable situation for the high tail (but how this is affected by socialization and cultural expectations is a topic for another post).
The evidence on that correlation is actually very strong. However in our society there is an effect that goes a long way to hide it. For a number of reasons (including earlier puberty), women have a significant academic advantage in high school. This means that about 60% of people heading to college are women.
So if you're in an environment with lots of young college educated young people, all will be reasonably smart (they had to be to get into college), and you have on average about half-again as many women as men. If you just take this population and look for the top quartile, women are still over-represented relative to men.
What about the smart men that I said existed, where are they? They are everywhere. It turns out that if your IQ is in the top 2%, you have worse odds of finishing high school than if your IQ is median. Lots of smart people make it nowhere near college for various combinations of reasons. If you mostly hang out with college graduates, you might never notice that, for instance, there are some really smart car mechanics out there.