I've said it before and I'll say it again: In a straight-up fight based purely on his fighting abilities and whatever gadgets he had on hand at the time, Batman would pretty much lose to any of the super-powered guys (SM, WW, GL, etc). Because of this, I have to assume that Batman is going into each of these fights on
his terms, meaning he already has his contingencies and strategies planned out beforehand.
In the case of Flash, assuming Batman has prepared for the fight, I've got to give it to Batman all the way. Otherwise Flash could just disintegrate him before he even knew what was happening. If you're curious how a character like Batman can take down a character like the Flash, here's a panel of Prometheus (basically an evil Batman) taking out Green Lantern and Flash at the same time without breaking a sweat:
I should mention the entire thing about the bombs is a straight-up lie, but Flash has no way of knowing that.