The answer is, your mileage will vary. If you've got some technical chops (and a desire to exercise them) Linux should work fine in a workgroup setting, and the upfront costs can go into your pocket (maybe for some neat hardware upgrades). If you're Clueless about computing, if you want it done for you, then maybe Microsoft will work better for you.
Plus, it depends on what you're doing with it. There are great Microsoft applications in some niches. There are perfectly fine Linux alternatives in others. And some just gotta have a Mac.
Frankly, I think the original Microsft "study" itself is the real news. You don't write a big check to a market research outfit unless you need to. And Microsoft would not have written this check, nor advertised the results, if it didn't feel it needed to.
The patch management process is something I've been yammering on about here for some time. It is something Linux folks could address and profit from. But is it a deal breaker? Not if you've got someone on staff who knows what they're doing, no. Not if you know what you're doing.
Linux is not yet idiot proof.