Just my 2 cents here, I notice most of the posts against using IDEs refer to the older IDEs. They still bring up viable arguments (i.e. invasiveness, vendor-specific libraries, etc.), but I've never had a problem dealing with IDEs generating their own code that I couldn't track down and I'm by no means a guru. Most IDEs nowadays still allow you to 'do your own thing', of course, I do completely agree that there's a huge learning curve (even IDE to IDE) and that newbies should start out using Notepad or Emacs.
I don't mean to go on a rant here...I could be wrong.