Building a site entirely with Flash creates some SEO problems, however using some bits of Flash within a web page is fine. Increasingly hardware is stopping supporting Flash though, as HTML 5 can do a lot of the same stuff much more cleanly and much more search engine friendly.
The important thing is that you have some standard HTML text on the page, that is what search engines can see and understand, they can't see flash at all, so you could make a nice animated header image for your page in Flash then have HTML text below it; that is fine.
Generally though, I recommend you look at HTML5 instead, it's the future.