This.
I don't know why a lot of people just assume that having Windows means you'll learn using Microsoft's development tools. Nothing's preventing you from choosing Apache over IIS, or Postgresql/MySQL over SQL Server Express.
Most major web app development platforms run on Windows, and there are plenty of good, free text editors too.
This isn't CS fundamentals, but, at least for a good portion of CS 1 classes taught at my school, and all of the CS 2 and data structures, Visual Studio is what people are taught, with the OS X users typically using XCode.
I don't know if it's better to start with IDEs or just basic text editors and compilers, but I know a lot of CS majors are going to be coming out of my school without knowing how to compile and run almost any program without clicking on the green run button in their IDE.
CS fundamentals can be taught on any system. Most kids don't have really technical people in their lives to get them past some of the hurdles of even getting started. I think we sometimes forget that the whole world doesn't want to be Linux gurus -- they want to be able to watch their cat videos and check their Facebook accounts. Most people don't care about the technical parts. If we can try to make the more technical parts accessible to a wider audience, I think that's moving the needle in the right direction.