I read an interesting article called "Why Flash is Mostly Bad". Since I began designing in flash years ago, I've become pretty familiar with the major pitfalls associated with designing in Flash. I got my start when 100% Flash websites were common and desired. . . the web's come a long way.
I think Flash has its place. The New York Observer has some really cool Flash bits -- check out the "Observed Today" block especially. Even the top stories widget is cool. But that's the point, isn't it -- they're just widgets. If the user doesn't have Flash installed, the site doesn't break. Sure, they can't see some neat pieces (and those pieces add value), but are they locked out of the site completely? Not at all.
That illustrates the division between two schools of thought, in my opinion: using Flash as the base of your site, or using it as widgets that add value to your already-accessible site.
For every Observer site that does it right you'll see 100 sites that employ mystery-meat navigation, re-write your scroll bars, have background music you can't turn off, or don't let you in at all. Is Flash "mostly bad"? I don't think so; Flash is just a tool. Blame the author, not the pen.