I'm a math professor at the College of Charleston. Just so you know, the College of Charleston is a comprehensive liberal arts & sciences / professional / master's university with expectations that faculty do research, but we don't have an engineering school, so our IT group as a whole gets away with stuff that would never be accepted at a research university or any institution with an engineering school. Our students don't have any network drive space, for example. The computer science department has a Linux cluster that several departments share, but they maintain that themselves. I'm in mathematics, and we have one professor who serves as an admin of sorts for our Mac lab, but otherwise we have no department-level IT resources. Our college-wide IT system has a reputation for being underfunded, understaffed, underpaid, and overworked. It's not just Linux that we have problems with-- the support for Mac OS X was pretty bad until recently, and a lot of the problems I'm having affect Mac and Windows users, too. A lot of what I'm about to spout isn't entirely IT's fault, but they do contribute. Some of it is self-inflicted because I insist on doing things The Right Way and I'm impatient.
That said, this is my situation as a Linux user here:
Officially, the college uses Linux for web server stuff, research computing, and some of the IT staff use it, but there's no official support for other users. I run Fedora Linux for personal preference reasons and for research reasons, and when I have a question I can't answer on my own, someone in IT or the computer science department usually eventually answers.
The big problem is not so much lack of official support, but rather that various parts of our IT infrastructure are constantly in my way, which means I have had to spend a tremendous amount of time and energy building solutions to what should be simple problems:
* I had rig my own backup system. The college provides a backed-up faculty network drive, but it's on a Windows server and there are files that I can't just copy over because of file name restrictions, and it doesn't keep up with file permissions and ownership, etc. So my little experiments with rsync escalated into me making a Linux file system inside my Windows storage space, which involved learning all about LVM, /dev/loop, mounting file systems with barriers, all kinds of neat stuff that isn't my job...
* We have a few applications (the VPN, the course management software) that are supposedly platform neutral, but require applets that don't work with Fedora's distribution of java. Getting the Sun / Oracle java plugin installed and working was way too much work for me: the poorly documented non-installation of libnpjp2.so, having to disable the stack-is-not-executable SELinux feature...
* The now-replaced horribly obsolete course management software didn't recognize web browsers with "Linux" in the user agent information, and would pop up a window and demand that I click OK for *every* *single* *click*. And it was a Web 1.0 type of system, so you had to click a link to do anything. It drove me nuts. I had to figure out how to make Firefox sent fake user agent information.
* The entire campus is behind an ultra-paranoid firewall. You can't just SSH to a research machine from the outside, you have to go through the VPN. We're on our third VPN solution, each of which claims to support Linux. The first one worked very well but for some reason they couldn't continue to use it, so we've been through two others, and for both the configuration and fixing I've had to figure out and do has been monstrous: installing java, compiling obsolete versions of openssl, setting up VNC to compensate for absurdly short time-outs, enabling third party cookies, and on and on...
* Faculty e-mail is on Exchange, and IMAP is available, but they won't tell us how to configure an IMAP client like Thunderbird. (Evolution can read from Exchange directly, but I had some problems with it.)
* Wireless had a lot of problems in general campus wide. I thought for a while it was just me and the Linux driver for my network card, but it turned out to affect a lot of other things too. That's been improving lately.
* One of our nameservers was broken, and for some reason the problem didn't show up in Windows, so it didn't get fixed for a long time. So here I am hacking away at /etc/resolv.conf every so often when DHCP overwrites it just so I can check e-mail...
* Our IT poobahs want every issue to go through the main help desk to be triaged, but there are many layers of people there who don't have a clue what I'm asking for, and I end up solving most problems myself by the time the request has been "escalated" up to someone who does and who finally has found time to consider it.
* I've heard buzz about student projects, like writing a web database, that crashed and burned because of security and other policy problems.
Recently our IT grand poobah held a meeting with a bunch of faculty and asked what IT can do to support high-performance research computing. I was just about ready to scream, but I held my tongue. I also just had a meeting with our network engineering people, and I'm cautiously optimistic that there might be some improvements in the works, but it's going to take a lot of time, and so much damage (as far as me wasting time on stuff that isn't my job as a mathematician and teacher) has already been done...