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.
All the above answers are focusing on Flash, Silverlight is just as bad or worse. If you are running Firefox with NoScript (you should be) then you have to click on every script that you wish to allow to run.
So build your websites with scripts, Flash and Silverlight. Just make sure that they still work with them disabled. Many of us will simply move on when we open a site and see nothing.