Merchandise revenue is divided among all the teams. If San Antonio got a team, they'd probably sell more San Antonio Widgets gear than they sell Cowboys gear and Jerry Jones would make more money. Jerry Jones gets 60 percent of the gate on all home Cowboys games, which are almost always sold out anyway, and people from San Antonio aren't exactly taking up seats that would otherwise go unsold. Unless they're buying a load of luxury suites, they don't factor in either.
If San Antonio got a team Jerry Jones would be happy if it means more money for the Cowboys, and he'd be happy for Jerry. There's a case to be made that a team in SA would be financially beneficial to him, so there's no reason for him, or any other NFL owner, to oppose it. Beyond that I'm quite sure the city rarely enters into his thought process. Those people that think he's expending any effort to prevent them from having a team think far too highly of themselves.
Five of the top ten most populous cities in Texas are in the DFW area. San Antonio means slightly less to Jerry Jones than Mesquite or Carrolton.