It's a valid angle IMO but EA actively support editing on the consoles for NCAA - giving known roster editors early copies, keeping editing an option etc. They know without editing it wouldn't sell nearly as well. Plus as far as players go, you can't edit much more on the PC anyway. I mean once you've got the names down the personal stuff pretty much ends there. It's just easier on the PC with a mouse and keyboard.
Anyway, for my take - I think it is primarily about circumstances. Back when the PS2 was new, EA were struggling to port Madden to the PC without major performance issues plus, as I said above, it was always a year behind features wise until the Xbox version was made (as Xbox to PC is way easier than PS2 to PC). Under those circumstances I doubt NCAA would have sold much on the PC at all. EA got their PC act together (relatively speaking) around Madden 04-05, and by then they probably figured it was too late in the cycle to bother bringing NCAA back.
I think there is a slight possibility NCAA could be brought back to the PC in the near future, but only a very slight one. Profit is a factor but I don't think it is the biggest factor - NFL Head Coach is a tiny seller and they're making another one, on the PC, for 2007, and that was an original creation, not a port of a pre-existing series. Porting an Xbox 360 game to a PC and getting it up to scratch is not a big deal, they could do it with pretty minimal costs and I seriously doubt it wouldn't profit. This is why I think there is a slight chance still - the average PC is not quite ready for Xbox 360 ports yet (at least not from notorious poor PC optimizing companies like EA), but when it is, NCAA might come back because Microsoft have made easy 360 <> PC porting a priority this generation.
The question then will be if EA will still bother though. I sincerely believe EA would happily stop PC production altogether if they could. They don't strike me as a company interested in expanding on the PC at all really, mainly because a high up executive basically said as much.