But it WASN'T funny. And it doesn't seem like he INTENDED it to be funny -- his defense of it hasn't even been "Come on guys, it's just a pee joke, what did you expect from me?", it's this trying-too-hard "I've talked to firefighters and it happens in stressful situations, even to the bravest people in the world." (Although he DID kinda give a mocking-the-fans "And DC let me print it and it's canon now, so haw-haw." Which is childish but what the hell, fans who obsess over canon totally deserve to be mocked for it.)
The context of the scene isn't that it's a cheap joke. It's Batman, in a moment of vulnerability, admitting something embarrassing to a new hero who is self-conscious that he doesn't have what it takes. Its importance to the story is that Batman is starting to trust this guy and open up to him.
Which makes it all the more weird and out-of-place.
(Also at the end [spoiler]the new guy turns out to be Smith's awesomely-named-but-lame villain Onomatopoeia, and as soon as Batman trusts him enough to bring him to the Batcave and reveal his identity, Onomatopoeia turns around and fridges his girlfriend.[/spoiler] Really, what the fuck, Kevin Smith?)