Perhaps he was just really interested in capturing fruit flies, like me? What, am I the only one fascinated by this? I've got like 30 of them in one trap, right now. I could sic a small fruit-fly plague upon your house, if that was what I wanted to do.
Fly-bottle is like the glass version of my little fly-snatching contraption. And the fly is the person interested in asking philosophic questions, tricked by language into asking such questions in the first place. Wittgenstein would prefer that we just stop doing philosophy and realize the unimportance of such questions, thus finding our way "out of the fly-bottle."