What screen resolution are you using?
Did you un-install any fonts from your system?
Did you mess with Safari settings using a 3rd party application (Saft, for example)?
Could be lots of things.
From all the browsing I've done over the last 4 years using Safari, the only websites that gave me problems (very few) were poorly coded or relied on Windows ActiveX standards.
When I visit a website that does not support Safari or even Firefox, I just leave. If the webmaster does not bother supporting major browsers, I figure his site is not worth my time. I wouldn't complain if I were using an obscure browser but come on, the Mac market share is pretty important now, and rising fast.