This may be one of those traditions whose exact origins are unknown.
"One tradition, unexplained, is the tortilla toss. Runners, about 10
percent of them in costumes, tossed hundreds of tortillas into the air
like Frisbees, blending in with the news helicopters."
I suspect that this article is correct: the tortilla-tossing is just a
way for the crowd to pass time, similar to balloon-batting at rock
concerts. And tortillas, unlike balloons or Frisbees, are
"A part of Bay to Breakers that distresses me every year is the
deplorable 'tradition' of hurling thousands of dollars of tortillas on
the street to be swept up as garbage, a wanton waste of perfectly
edible food, in the service of frivolity.
I know it started out as a humorous equivalent to batting balloons
around at rock concerts; people lined up waiting for over an hour at
the starting line could amuse themselves by frisbeeing soft harmless
tortillas at each other."