While many people don't like Flash, there are some good reasons to use it. It is an easy way to add amimation, games, and movies, it provides clean vector graphics, and it's widely supported by Web browsers. But there are some things you should never do when building a Flash website. If you do these things, you'll lose more customers than you impress.
Flash is Slow to Load
If you've built your entire website as a Flash SWF file, this can take a long time to load. On one site I visited, the only thing that displayed for the first 10 seconds was a headline and side navigation (in HTML), and I'm on a high-speed connection. When the Flash finally loaded, it loaded a count-down timer to tell me to "please wait" as the Flash page loaded. So they wanted me to wait 10 seconds so that I could see their count-down timer? Wow. In most situations the count-down timer wouldn't have made it to 0 before I'd hit the back button.
Flash for Navigation Creates Hard to Use Navigation
While Flash is widely supported, many people still find it difficult to use, and putting your navigation in Flash is just asking to confuse them further. Flash navigation is hard to use because it's not "normal". Most people are familiar with Web links and buttons as well as the back button. But Flash navigation systems typically use some other method. I have seen sites that completely hide the navigation until your mouse happens to slide over it (like the optional hidden doc in Macintosh computers). Other sites use navigation that isn't standard like photos or even video.
You can set up Flash navigation with links and buttons that look like typical Web page navigation links and buttons, but what is the point? Flash is harder to edit than plain HTML. If you're going to put your navigation in Flash but make it look like HTML, why not just make it easier for everyone and put it in HTML.
Flash Looks Like Advertising
Partially because many ads on websites are done with Flash and partially due to how the designers built the Flash, many Flash websites end up looking like an advertisement instead of a place to find information. On one Flash site I visited, the main section of the site is a rotating banner advertising a grand opening, a giveaway of a car, and then finally their company. I nearly scrolled past the rotating banner because I thought it was an ad - but it was the site content!
Flash Disconnects the Back Button
Most people browsing the Web use the back button as their primary navigation aid. But when you enter a Flash website, often the back button is disabled or non-existant. In other words, you click from one page to another inside a Flash website, but if you click the back button, you end up either on their home page or even back in the search engine where you found their site to begin with.
When you create a Flash website, you need to give people a way to navigate within it without having to start from the front page. For example, one site I visited had a catalog of products in their Flash website. If you went to the first category page you could see all the products in that category. Then you choose a product to view more information about. But there's no way to get back to the category page you were just on. You can go back to the main page and then click through the catalog again, but you can't hit a back button and keep browsing from your current place. I gave up fairly quickly, rather than browsing through all their inventory.
If You Have a Flash-Free Option, Keep it That Way
Once someone has chosen to view your site without Flash, they shouldn't have to choose that on every new page that they load. On the site I was visiting, I could click HTML navigation to get to various sections of the site. Once in a section, the Flash would load for that section and at the bottom would be a tiny "view as HTML" link. That meant that every page that I went to loaded Flash that I didn't want, even after I'd chosen the "view as HTML" option.
Flash Can Be a Useful Tool
But you need to think of it as one tool in your Web design arsenal, not think of every situation as another opportunity for Flash. As Mark Twain would have written "To a man with some Flash skills, everything looks like a Flash application." Move beyond Flash - use it when you have a nail that needs hammering, not whenever you have the chance.