There's no problem in that (to each his own...) but it has nothing at all to do with "1% marketshare" and "linux kiddies don't wanna pay" bullshit.
AS a former user of both Cadence and Mentor tools, just talk to anyone inside their company. Virtually all the licenses are for Windows now. The crowd who demands Linux aren't running around with fist full of bank notes ready to through it towards Mentor or Cadence.
In a different segment, I know of a couple companies who offered tools for Linux (Freescale being one.) who offered their tools for Linux. They eventually dumped it after a few releases as there was almost no uptake compared to the full user base. The ones that did had no interest in the paid version.
As far as Xilinx, the Linux versions for Vivado, ISE and Chipscope have a bit more uptake but I have found that the drivers for the hardware are awful and some features are disabled. Once again, most of actual sales goes to the Windows users.
Just look at the ancedotes on this forum. Everyone balks at the idea of Altium charging while simultaneously wanting Linux. Sorry, no one with a financial brain would spend any effort porting for a group who believes all software should be free. It only makes sense if you start with toolkits from day one that make porting and testing easier.
Even if you do that you end with a GUI that looks and runs like shit on all platforms. Just look at Eagle, et. al.
A tool really on needs to work on one platform well. If a user is unwilling to pay (Especially if the software cost is significant) a little bit of money to get the OS, then they are a shitty customer with other political motives. Engineering is not about religion or politics. Be programmatic and use tools to get things done. Case in point.... I play and record music. I find that Logic works best for my workflow. Instead of dicking around looking for Windows or Linux alternatives, I simply get the platform that supports what I want. I didn't have a Mac. Guess what? To support my hobby, I busted ass for awhile to get the cash and bought the tool I wanted.
If the tool was written for some strange linux flavor, I would just go that way. The last thing I want is the developer spending time on porting to every platform in existence. That time could be better used adding features and fixing bugs, not doing regression testing on all the different platform variants. Just make the tools work in one environment well.