I work in IT for a college campus that has both Macs and Windows machines.
Windows has Remote Desktop and Remote Assistance, which means we can do A LOT of stuff from our desk. Usually, unless it's a hardware problem, or huge software problem, we don't have to get off our lazy asses to fix something across campus. Remote Assistance is great for helping out users because we can see their screen and control their computer. You need to pay for Apple Remote Desktop, and I'm not even sure if there's a Mac equivalent of Remote Assistance. At least not something that's free. Both are built into Windows. With the Mac users, if they need assistance and they can't be walked through on the phone, or if they need something installed (which we, as administrators have to do), they need to wait for a technician to come out to their office. Depending on workload, this can take up to a week. With Windows, we can do it for them immediately when they call.
Macs don't support our DFS network shares. Say what you want about it, but DFS is one of Microsoft's better products. It works great from a server standpoint, and it's even better from a user standpoint. Our users just love the fact that they can go back and restore old versions of files. And don't even mention Time Machine. We're not setting every Mac on campus up with an external drive. DFS's shadow copy is all server-side. The only way to get to the network drives on a Mac is using an SFTP client, and that's just cumbersome.
There's no good Exchange client for Macs. Entourage is clunky. Mail doesn't support Exchange tasks, notes, contacts, calendars, directory, or anything else besides e-mail. Why Microsoft can't just port Outlook like they have with Word, PowerPoint and Excel is beyond me, but until there is such a thing, once again, Windows wins here.
Most users have Windows at home. So they're comfortable with Windows at work. Why re-train them on the basics of OSX when they know their way around Windows? People say Macs are intuitive and easy to use, but I've answered what we here would consider dumb, newbie, RTFM-type questions from my coworkers in IT before regarding Macs. I question the intuitive-ness, especially when you've been used to Windows your entire life. There's a learning curve, just like anything else, and some people just have difficulty learning. It took them long enough to learn Windows, might as well let them keep using it. Saves us and them many headaches.
Most of the software used by students and employees is Windows-only. The security guys, except under certain circumstances, will not allow dual boot or a virtual machine to be used, because the secondary OS, in this case Windows, is not running that often, and thus, may not get a chance to download Windows updates and new virus definitions. The Windows computers are usually up 24/7 so they get a chance to update everything. And it's just not cost prohibitive for people to have one of each.
Finally, cost and upgradeability. The Windows PCs are cheaper. There's no denying that. And, we can upgrade just about everything besides the CPU without voiding Dell's warranty, so we can always throw in a larger hard drive or beefier video card and keep the computer in service a bit longer. And the PCs probably hold more RAM than the iMacs (the most common Mac on campus, very few professors have Mac Pros due to cost. There are a lot of MacBooks and MacBook Pros out there too, and some various PPC Macs as well, all of which have limited upgrade capabilities)