I've had this problem forever. Safari for OS X shrinks my fonts, but IE and FireFox for Windows do not.
Please check out http://www.stbedesantafe.org. If you have OS X 10.6.4, look at it in Safari, then look at it in Windows, Internet Explorer and Firefox. Most noticeable on home page. Any ideas are welcome.

All websites or just websites made with CoffeeCup products?

I have always noticed that myself. There is not a great deal that can be done about it I think as increasing the font sizes just ends up making them look clumsy in other browsers. You could always add a small note for Safari users to use their CTRL + to zoom in on the page I guess.

you could create a safari specific css and load it

<!--[if Webkit]>
<link rel="stylesheet" href="webkit.css"
type="text/css" media="screen" />
<![endif]-->