I think the idea that San Antonio can't support an NFL team is an archaic idea. San Antonio alone has at least 3 corporations that are, IIRC, in the Fortune 50: SBC, Valero, and Clear Channel. It has a coming influx of corporate money from Toyota. It also has some more localized and under publicized businesses that have been good in their sponsorship of the Spurs and other similar ventures, including: HEB and KCI. I'd be surprised if the similarly-sized markets in the NFL have substantially more corporate money than San Antonio.
I think one thing is true, though. San Antonio's loyalty to the Cowboys is harmful to its chances to get a team. The hullaballoo about the possibility that the Cowboys will be taken off of television in favor of a Saints game sort of points to the problem. If SA got a team (the "San Antonio Hypotheticals") and that team was in the NFC, Cowboys fans in SA would lose out on seeing the Cowboys for a number of weeks each season. That's the tip of the iceberg when it comes to Cowboys-related conflicts -- all of which would take from the local support base and make life difficult for the Hypotheticals.
I stand by my position that San Antonio, by and large, supports the idea of getting an NFL team, but would prefer that that team be the Dallas Cowboys.