SFO was selected both because it is one of the busiest commercial airports and has intersecting runways.
The judge's ruling said the travelers have not shown that they personally would be harmed enough to stop the deal from moving forward. Seeborg wrote on Monday that none of the plaintiffs testified to having flown regularly, and that only one said that she is likely to use United or Continental when she does fly.
The Justice Department has already said it has no antitrust objections to the deal.
United spokeswoman Jean Medina said the airline is pleased with the judge's decision.
Shares of UAL Corp., United's Chicago-based parent, rose 18 cents to $23.02. Houston-based Continental Airlines Inc. added 4 cents to $24.15.