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.
Look at any major car maker's website, they are ALL in Flash. It depends on what you are doing. If your goal is to provide a rich, sexy website Flash/Silverlight will give you a huge advantage in terms of development time. IF you are providing content/data HTML and JavaScript (jQuery for example) can give you a lot of whizbang without requiring additional software plug-ins (Flash/Silverlight).