If a tool such as APT-GET or YUM or RPM or YAST or PKG_ADD connects to a central bunch of centralized servers.. this can be a weak point..
No unix systems have 'virus checkers' on them because unix so far has been fairly unpopular compared to windows. It has nothing to do with permissions or security.
So someone hacks/cracks into the debian servers and infects 352 packages with a unix virus that makes all 352 of those packages run through your system and delete every file with permissions on it that can be deleted.. and it even tries to trick you into logging in as root with a prompt "in order to install this package, you must enter the root password to change some settings in /etc/'.
Why has this not happened yet? Oh it will.. a centralized package system is a big danger.. just like gasoline is a big danger.. it just a matter of time before someone lights the match. So far, not many have lit the match.. and unix is full of friendly nice people that don't create viruses.. but believe me, it will happen.
Any tool that is POWERFUL is dangerous.. and centralized package systems are very very powerful. They are also very centralized, which is the weak spot.. viruses spread easier when there is a central place that everyone connects to (without any condom, since Unix doesn't need a condom, people think (and even condoms don't stop the viruses some times)).
Smart security experts that are in the know... laugh at those who say yes unix is more secure! Much more secure!". No. Unix is much less popular... that's all. Has little to do with security.. Unix is more powerful than other operating systems and is therefore LESS secure in many ways.. maybe slightly more secure in some ways.. but much less secure in other ways.
The only way to stay secure, is to disconnect your computer from the internet and stuff all your serial ports and usb ports with kleenex so no one can connect to your PC... and even the kleenex won't work very well as a protective measure...