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You raised enough that he didn't have the right implied odds to fish for a set. That means that even if you go ahead and pay him off when he hits one, it's still a mistake for him to call pre-flop.

I generally don't like raising a larger than ordinary amount with AA, because I think it sends up red flags, and I don't want my opponents to know I don't have AA when I make a standard raise.

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True.. but your assuming the 99 knew he was up against an overpair. Way to often I see overbets preflop signalling AK or AQ (though JJ comes up occasionally too). A flop of a 9 OR all undercards (or no A or K) could have been exactly what the BB was looking for as he did not put you on an overpair.

Which brings up the dilemma of AA.. bet to much and you get no action... bet to little and you give the odds to be drawn out against. Hence the saying, "with AA you usually win a small pot, or lose a massive one"