I think this should have been "With the rise of the Linux desktop, will malware follow? " and the answer would have been yes. Any OS written by humans is inherently insecure. This means someone else will find those insecurities and attack them.
Anyone who thinks their OS is "safe" is stupid. It just depends on (a) how many instances of this OS are accessible which determines (b) whether it's financially worth developing attacks. If (b) = yes then someone will.
I think the human is now becoming more of a target than the machine; why spend ages figuring complex ways of silently stealing data when you can flash up a big "You have a virus! Buy this software now!" sign in a web browser knowing that a lot of people will just accept it and spend the money? That's much easier...
If you want your workstation to remain secure, don't ever plug anything into the back of it. That way you should be safe.
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