The article makes some pretty bold claims about Linux getting a virus. I admit, I'm quite skeptical of the conclusions the author makes. I do security work on Linux and I keep telling everyone "our day is coming". I won't complain if I'm wrong, but I suspect I'm not.
Here are my thoughts on the issue.
The reason Linux doesn't have viruses is because Linux doesn't have viruses
This basically means nobody is really writing them. Why not of course is up for debate, but even if they didn't propogate well, we'd at least see something out there. So far there's not much.
Your phone is bigger than the Linux Desktop
I expect every year for the next 50 or so to be "The Year of the Linux Desktop". What a lot of people don't get is the desktop is becoming less relevant than ever before, but Linux is more important than ever before. Watch out for viruses on your phone, that's the next place the bad guys are going to go. Except this time it's not going to be about telling all your friends you love them, it's going to be about stealing all your information and money, THEN telling all your friends how much you love them.
People are the problem
Fundamentally speaking, until we remove people from the equation (which is pretty hard to do and still turn a profit), we will have attacks. While some platforms do make attacking them easier than others, I'm fairly certain in at least 80% of instances it was a person making a bad decision that caused their computer to become infected. Technology moves faster than people can learn, what was safe today won't be safe tomorrow. We can't even imagine what the next attack will look like.
Will Linux have viruses? Maybe. Will Linux become a bigger target? Certainly. Can we do anything about it? Even if not, we're going to try. Buckle up, I suspect the next few years are going to be a wild ride.
Linux will never have viruses.. because people will keep redefining what Linux is to being something can't have viruses. I mean if we go with the GNU line we end up with Linux just being the kernel.. and well a kernel can't have a virus because it needs other stuff to get a virus and that other stuff isn't Linux.
After “Secure Boot” (i.e. restricted boot) is prevalent, and the operating systems are locked down to not allow anyone to sideload any non-OEM software, we could be completely free of trojans and viruses. That might be good for the average level of system security, but it would be a horrible blow to innovation, competition, and the indie/hobbyist developers.
The above statement is 100% false. Most common viruses affect the system after boot time. I.E With secure boot it wont make the slightest difference about the number of viruses available.
The article linkes seems to be full of flaws.
The article also goes on to explain how all the different distros are diverse and hard to target.
At the end of the day all distros run the linux kernel, stores most configuration files in /etc and it would be very simple to write cross-distro malware.
That being said however malware in linux will never be as common as windows malware. In my oppinion this is all due to the fact most linux users are more technical than others and use file permissions to control access to their system (i.e no world writable directories). The ones that are not that technical will mostly stick to the distro repos any way.