I have the feeling that Flash-based ( or Silverlight-based) websites are generally frowned upon, except when you are creating games or multimedia-content rich applications.
Does anybody know a site called YouTube? It wouldn't exist without flash. Flash has great video/multimedia capabilities that simply cannot be ignored.
Flash is amazing when used in the proper way, in appropriate circumstances and when the designer/coder has taken care to embed basic accessibility features.
The thing is, like all good things, there's a lot of abusive use (flashturbation). Especially in the beginning, when people just want to slap Flash wherever they can just to show off.
But I strongly disagree that Flash sites are bad: When made properly, and with good UI design and accessibility, they bring a whole new dimension to the web.