Linux boxes aren't the main target for quite a few reasons.
1. Persons running *nix usually have much more experience than your average windows user. This in turn means that they usually have more experience implementing better security than your average windows user.
2. Most major exploits for *nix are local, this means that you must already have some kind of access to a command line on the box to even try to execute the vulnerability. Sure more and more rce (remote code execution) exploits appear everyday, but this only gives the hacker access to a make-shift shell, and as I stated in point one, the average *nix administrator has more experience w/security, meaning most *nix boxes today have hardening patches installed (these tend to keep hackers out).
3. It is much harder to hide things on a *nix system. If you haven't noticed, there are many different flavors of *nix. This being true, it is much harder to develop a standard rootkit. Sure shv5 works on a portion, but there are hardly any for freebsd. In retrospect, if you look at windows there are numerous rootkits, backdoors, and ways to hide things away from the administrator. Ever hear of ntfs streams? So simple yet almost completey undetectable to the average user.
Also, if most 'hackers' targeted *nix so much it would get much more attention from the government. I guess you've never seen what 17 kaitens can do compared to a couple thousand bots. There are so many more reasons why *nix is a lesser target than windows to hackers, including one huge one that I didn't bother to mention.
EDIT:
To show how ridiculously insecure windows really is, here are a few public exploits:
http://milw0rm.com/id.php?id=1505http://milw0rm.com/id.php?id=1504http://milw0rm.com/id.php?id=1506http://milw0rm.com/id.php?id=1502http://milw0rm.com/id.php?id=1466http://milw0rm.com/id.php?id=1420http://milw0rm.com/id.php?id=1391http://milw0rm.com/id.php?id=1352http://milw0rm.com/id.php?id=1260aww hell, there's too many to list so I'll just link the whole thing.
http://milw0rm.com/parse.php?platform=windows