Any theater writer has probably had one or two flops. As a theater geek, I love flops. One of my favorites is the Sondheim-Furth 16 performance flop, Merrily we roll along. I like this show because of the exceptional score by Sondheim, and honestly I think it is one of his best works other than Into the Woods and Sweeney. So what is your favorite flop? I'm pretty sure all of us have at least one.
Timbuktu, an opulent, all black revisal of Kismet with Melba Moore and Eartha Kitt as Lalume, directed and designed by Geoffrey Holder. It was wonderful but got mixed reviews and sank within a few months.
Fantod, I don't think that Peter Pan flopped on Broadway unless your talking about one of it's revivals. Heck, the musical spawned four TV versions and three revivals, I'd call that a hit.
The original Peter Pan only ran for 154 performances, and while I don't have any official sources, I think that even back then you needed a longer run to make back your money.