A lot of people are bringing up the whole malware/viruses issue alongside performance issues as well. What I haven't seen mentioned much is that *IF* Linux were the mainstream OS on the desktop you would see a lot more malware and viruses for Linux distro's. I mean hell Android alone has been hit so hard with malware and viruses it's become more of a joke then anything especially when some of it comes from the official google play store hidden in various apps. Same applies to Mac OS/X which also has seen an increase in malware and viruses the last few years.
Hell even MS-DOS back in the 80's and 90's were affected by viruses when that was the mainstream OS and when Windows 3.0x and 3.1x releases came about we started seeing more viruses affecting them and then it took off with Windows 9x releases and so on and so forth. Heck let's even say if Microsoft and IBM had decided to play nice years ago and kept co-developing OS/2 together and had released that in 1990 instead we might have been in a world of Microsoft OS/2 today and still dealing with viruses and malware.
Part of the problem is that Microsoft encouraged bad computer user habits for the average user that unfortunately still exists today for most people who have no interest in learning how to defend yourself from the vast majority of shitware and viruses out there. Automatically clicking on file(s) attached to e-mails if using Outlook, downloading various free, trial, or even commercial programs, especially from CNET, where it's bundled in with so much adware/scareware/crapware/malware you name it, that you have to uncheck several boxes and click through more prompts to confirm that, yes, I do not want this toolbar or this search engine or this software installed. Even now some uninstallers try to install more adware/malware when you remove the original program which is just downright nasty.
Then we wonder why so many people are (or should be using) programs such as Malwarebytes Anti-Malware, Spybot Search & Destroy, and at least a half assed decent anti virus like Avast if you need realtime scanning, or Clamwin AV if you just feel the need to scan executable files you download along with a decent firewall such as Privatefirewall or, god forbid if you like buggy pieces of shit firewalls, Comodo or Zonealarm. And linux users arent immune either in that sometimes people who arent familiar with the terminal will randomly copy and paste sudo command lines from various "Linux help sites" to install this program or that and don't verify that what they are copying and pasting is actually what it says on screen. I mean hell you could have it say onscreen "sudo apt-get netflix-desktop" but when pasted into terminal a user in a rush might not realize it says "sudo apt-get malware-sucker-package" and boom your linux box is now targeted for god knows what.
Same goes for the browser too. Too many people still use Internet Explorer which for over a decade now has been so full of security holes its no wonder windows systems get fucked up so hardcore. Using firefox along with Adblock plus, Noscript, Ghostery (or DNT+ if you prefer) goes a hell of a long way on windows to stop a lot of the "visit said website or get re-directed to a website and have software installed without your permission" often through something as innocent looking as flash ads, banner ads, or sites insisting you have to "download codec to play video" when you don't need it to do so.
And finally for performance it's easy enough to tweak in both Linux and Windows. Disable services and startups you dont need in both operating systems, honest to god de-fragment your hard drive in windows once a month even with free programs like Defraggler, keep the registry clean and learn what the hell is running in both operating systems at boot time, and what you have installed. I still have friends who don't bother to learn how to tweak windows or linux, how it all works, how to keep it operating smoothly and malware/virus free especially when browsing even if you use firefox and or chrome and don't have critical plugins/extensions like ABP and Noscript to give you better control, and then wonder why they have tons of toolbars and popups in firefox and chrome, and several toolbar and other "apps" in control panel and why windows 7 or 8 is running like a piece of shit exhausting RAM and swapping to the swapfile like a mofo slowing it all down.
In short if people would stop actually learn more about how to use Windows and various linux distrubitions safely and practice safe browsing to defeat all the ads and drive by viruses/malware that comes with those ads to begin with, and not drink the microsoft kool aid that tries to convince you Bing and Internet Explorer are the "shiznit" of the web, we'd all be better off. But because a lot more apps have been made over the years for MS-DOS + 16/32/64 bit Windows apps then any amount of native linux apps combined we will all be pretty much stuck using various version of windows as a main desktop, using virtual machine solutions to run software that may be 10 to 30+ years old, or dual boot systems even.