There are usually two different contexts of Flash on a web site:
Allow me to hit on both:
A full Flash web site is a complete no-no for a serious site. The only time it seems okay to use is on a brochure site for a movie, artist or maybe a web design firm. But seriously, full Flash sites were cool like 5 years ago when nobody actually cared about usability, consistancy, ease of use and a number of other vital aspects. Here are a few of huge disadvantages a Flash site has compared to a straight up HTML site:
Yes I am aware you can do some weird #url thing that does create a unique URL for each page but 99% of Flash sites don't do that.
There is generally no content on Flash sites as they are mainly animation and images. The actual text that they do have is worthless as far as making an assumption about the page - that is, if there even is a page.
It is almost impossible to do anything with content on a Flash site if it does have any. What are you supposed to do, bookmark the whole web site? How do you like your friend to the page, link him to the root of the site and tell him where to click?
Flash banners are fine for SEO. In this instance it is pretty much treated exactly like an image. It's just a blank area of content that search engines just pass over and move on. It can be embedded in an HTML page perfectly fine and does nothing to the overall structure and organiztion of the site.