The trick is that the question didn't have anything to do with women or the perceived "gender gap" (which, as Democratic activists will tell you, no longer refers to differing pay for the same job, but rather the aggregate income gap between women and men; men make more money total than women, even though they get paid the same for the same job (i.e., fewer women have high-paying positions than men)). If Nadella was asked specifically what "women" should do, he converted it to "people" in general, and his response had nothing gender-specific in it at all, and it really is a question that's equally applicable to employees of any gender or race.

It's an early gaffe from an otherwise politically-savvy CEO. Next time he'll know not to bother with minor appearances such as these, because it's not worth the cost.

EDIT: So it's actually a very long-winded question and employees not asking for a raise is the explicit subject of the question. I'm transcribing it from the video that eli linked to below (thanks for the link) so that we can see the full context. I'll transcribe the answer too.

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Q (interviewer): So one of the questions that somebody asked was how do you-- what do you advise to women who are interested in advancing their careers but they're not comfortable putting themselves up for promotions or advanced opportunities? And there was an interesting-- I just came from the Most Powerful Women's Summit in Laguna Niguel, and some of the other people here also made that trip to Phoenix, and there was someone who was talking about the fact-- it was Mary Barr, who is probably someone whom you're familiar with as well, and she was talking about the fact that she had never asked for a raise. And then her interviewer looked out at the audience, which was a lot fewer people than here, and asked "How many people had never asked for a raise in their life?" And I would say about a quarter to a third of the attendees raised their hands. And an interesting one was Warren Buffet-- and don't ask me why Warren Buffet is at the most powerful women's summit-- apparently he's been doing it for many years. So, you know, for women who aren't comfortable with asking for a raise or sort of saying-- who aren't the younger you, let's say-- what's your advice for them?

A (Nadella): You know, the-- the thing that-- umm, perhaps most influenced me in terms of how you look at the journey or the career. There was this guy, whose name was Mike Naples, he was the president of Microsoft when I joined, and he had this saying where he would say, "Look all sys-- all HR systems-- are long-term efficient, short-tem inefficient", and umm, I thought that that phrase just captured it, which is that it's not really about asking for the raise, but knowing and having faith that the system will actually give you the right raises as you go along, and that I think might be one of the additional superpowers that quite frankly women who don't ask for a raise have, because that's good karma! It'll come back! Because somebody's gonna know, "That's the kind of person that I wanna trust! That's the kind of person that I reeeally want to give more responsibility to." And in the long-term efficiency, things catch up. And I wonder, and I'm not saying that's the only approach, I wonder whether taking the long-term helps solve for what might be perceived as this uncomfortable thing of, "Hey, am I getting paid right? Am I getting rewarded right?", because the reality is that your best work is not followed by your best rewards. Your best work then has impact, people recognize it, and then you get the rewards, and you have to somehow think that through I think.

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In context, there is some specificity to this question. The interviewer asked him what he'd say to women who are too timid to ask for raises, and he said they're in a good position because you shouldn't be asking for raises anyway, and then went on to elucidate very general principles about how high-quality works percolates through the organization before it results in increased long-term rewards.

The interviewer continues to state how she'd been hired by other women at 50k under market because she said "just pay me whatever you want", and encourages the other attendees to learn to negotiate salary. Somehow I don't really see how this is a gender-specific issue at all. Lowballing an employee like that would've been seen as a win for the female hirer, and it happens just as much if not more to male employees who walk in and say "Please mistreat me" as this interviewer did. This also has nothing to do with the question of requesting a raise when you're already employed.