I wouldn't be so sure that the sites have a problem as wide spread as you might think. I used to run a mail server years ago and would constantly get put on the blocked list because some dumbass user would get a virus that would send massive amounts of email which relayed through my system. As a result I would get a free entry into the spamhaus.org bad sender list. Then I had to track down the culprit, correct the problem, and apply for removal from the spam list so other users could email domains such as yahoo, aol, msn, etc.
I would think that the "site is not safe" messages are generated by a list that is constantly updated. I know that Microsoft, google, and others have lists of "dangerous" sites that get flagged when you visit them due to them being dangerous. (look at
http://code.google.com/apis/safebrowsing/firefox3_privacy_faq.html for an example of what I'm babbling about ). If nobody has applied for removal from these lists then end users (that's us) would still be getting the warnings and whatnot. The only site that was flagged when I was visiting them was the skatterman & snug brim page. If nobody attempts to get the sites removed from the lists then I guess they update the entry for that site on the bad site list whenever they get around to it.
If you have a broadband innerweb connection then most likely you will have an ip address which is almost always online. There are many automatic scanner programs that constantly scour the ip ranges of broadband users. i always had problems with china, russia, and italy. My computer wasn't doing shit but sitting there and mothafuckas was trying to take it over to make irc channels and whatever else these wierd fuckers do.
Furthermore, Microsoft commands about 90 some % of the end user desktop space. That is one of the main reasons they are constantly targeted with malware, spyware, viruses, etc. The programs written for windows systems will have the largest overall impact and yield the largest overall results. I personally run ubuntu on my machine after constantly getting pwned by some fucking hacker fucks. Get an external drive and copy all your shit to that so you can reinstall your operating system without losing any of your data. Regardless if your running windows, mac, linux or whatever... backups are always a good idea.
Then again I could be wrong and the site could be purposely attacking your computer just to infect your shit and make your life difficult.... but I doubt it.
*EDIT*
I almost forgot to put anything atchually useful in this titangraph
If you run windows you can download SysInternals for free at
http://technet.microsoft.com/en-us/sysinternals/default.aspx
It will provide you with tools such as regmon which can show you what registry keys are getting accessed while your system is running or when you launch applications. They also provide other tools like process monitor which will look much deeper into your system then the task manager does.
Viruses, Malware, Spyware... that shit all sucks... but don't forget about rootkits
http://www.securityfocus.com/infocus/1850 they take the cake.
rootkit revealer might help
http://technet.microsoft.com/en-us/sysinternals/bb897445.aspx
If you feel up to the challenge you can download wireshark for free
http://www.wireshark.org/ Wireshark lets you set your network card to a mode that will see everything travelling across the wire on your network. It's kind of crazy and shit but it's a trip none the less.