Eh? Flash doesn't win anything; he gets straight-up shot in the chest. Prometheus only loses due to some questionable writing involving Catwoman and, I believe, Batgirl trading costumes to confuse him, allowing them to beat him in close-combat. No actual members of the JLA are involved in taking down Prometheus because he beat them all.
Your submission is that Batman beat Flash by setting up a losing dilemma. Batman didn't actually win anything, he forced Flash not to compete.
This is the stupid part of all Batman vs. debate proofs, most of them involve a specific scenario that merely disables his opponent. Batman hasn't "beaten" a ton of people he's tricked them or fooled them or just forced them not to fight anymore via extenuating circumstances.
The idea here is an actual fight between Batman and Flash. Even if Batman set up the exact same situation (motion sensor bombs, true or not) Flash wins the fight because now there is no collateral damage. He has no reason not to move faster than lightspeed, unless Batman also brought a bunch of civilians to the fight to force Flashes hand.
Edit: This ironically is a particular slice of bullshit people use to hand free Ws to Flash as well, the assumption that simply because they can't hit him or because he can phase through harm he must obviously be the winner Well, even if Flash can't be hit there's no guarantee he can beat his opponent either. He could waste a day running circles around Shazam or Adam or Doomsday or even Superman, but there's no guarantee he could generate a punch kick or anything that would physically end the fight and most his most stellar techniques (ignoring bullshit like turning people to stone or "stealing" their speed or going back in time and punching them as babies) run the risk of killing Flash in the process.
Either way, its fucking pointless. Anyone can beat anyone. They aren't real and there are no rules.
Also, this is a fucking popularity contest why do people take it seriously.
