That's a double-edged sword. Make it easy to run Windows apps, and you make it easier for windows malware to auto-execute as well. Part of the reason you can safely waltz right through a malware-laden environment in linux without an AV is because its program execution environment rejects windows .exe files in the first place. No execution, no infection, no security holes.
Auto execute to what? I've had plenty of viruses for windows on my Ubuntu.. since you can run .exe files through Wine..
However whenever it tries to spread it would require root, which is at my discretion
"Linux systems are by no means infallible, but one of their key advantages lies in the way account privileges are assigned. In Windows, users are generally given administrator access by default, which means they pretty much have access to everything on the system, even its most crucial parts. So, then, do viruses. It's like giving terrorists high-level government positions.
With Linux, on the other hand, users do not usually have such "root" privileges; rather, they're typically given lower-level accounts. What that means is that even if a Linux system is compromised, the virus won't have the root access it would need to do damage systemwide; more likely, just the user's local files and programs would be affected. That can make the difference between a minor annoyance and a major catastrophe in any business setting."
" "Linus' Law"--named for Linus Torvalds, the creator of Linux--holds that, "given enough eyeballs, all bugs are shallow." What that means is that the larger the group of developers and testers working on a set of code, the more likely any flaws will be caught and fixed quickly. This, in other words, is essentially the polar opposite of the "security through obscurity" argument.
With Windows, it's a limited set of paid developers who are trying to find problems in the code. They adhere to their own set timetables, and they don't generally tell anyone about the problems until they've already created a solution, leaving the door open to exploits until that happens. Not a very comforting thought for the businesses that depend on that technology.
In the Linux world, on the other hand, countless users can see the code at any time, making it more likely that someone will find a flaw sooner rather than later. Not only that, but users can even fix problems themselves. Microsoft may tout its large team of paid developers, but it's unlikely that team can compare with a global base of Linux user-developers around the globe. Security can only benefit through all those extra "eyeballs."
http://www.pcworld.com/article/202452/why_linux_is_more_secure_than_windows.html
Through personal experience and learning from others, many others, even if you allowed .exe files with a virus it wouldn't be nearly the same as Windows.
I could be wrong and there's always a chance for everything, with the security architecture of Linux it would be way harder to do any significant damage.