What I do is just not care, and if it does annoy me, I never let the girl know that!
Just reply politely, "hey no worries that's fine," and then dont ask her out again, or at least leave it a while before you do. If. Girl is genuinely interested, she'll make sure you're aware that the reason she hasn't met up is genuine, she'll be worried that she's messed it up and wont want to come off as a flake.
I've been flaked on quite a lot, notably by one girl about a year ago, id slept with her a few times before she went cold, kept texting me giving me attention etc but just always flaked!
Anyway I got really annoyed, made it obvious to her I was really annoyed and subsequently made a fool out of myself!
Rubbish at the time of course but I learnt a valuable lesson!
The way I see it, going on a date with me is a decent offer! I'm not brad pitt but I'm not bad looking, I'm pretty good company, and if I do date a girl I'm a pretty good boyfriend. So if, for whatever reason, a girl isn't interested in that, I'm not going to spend too much energy or time trying to convince her otherwise.