My first few years of programming were all in Java/Eclipse, and I had an irrational fear of the java/javac CLI compile & run commands. I was completely incapable of modifying build and run scripts (which were customized by one guy at my company), and it was a huge gap in my knowledge. So I have lived this firsthand and can see the value in retrospect.

That being said, I did get a LOT done with the pure IDE (three years of school programming and a year of part time work). So there's something to be said for both sides.