As others have said, it is fine to be faster in your IDE than without it, that's kind of the point. Being able to use complex tools correctly to boost your productivity is an important skill.
However, over-dependence on IDEs can cause problems. Skills and knowledge you no longer exercise will fade away, and your understanding of some aspects may be shallow. A classic example is compiling and running on the command-line - almost every time I do this, I get something wrong (usually class path related), because 99% of the time I let Eclipse do it for me.
This doesn't just affect you when you're out of the IDE - if your knowledge of the complexities the IDE is hiding from you is shallow, then when it goes wrong (and it will go wrong, at some point) you will find it much harder to fix.
I handle this two ways:
Learn new tools in their most basic form. For example, I switched from SVN to Mercurial, but started with the command-line client rather than the Eclipse plugin. This made my understanding of what was going on a lot deeper, which meant I knew what was going wrong and how to fix it when the IDE threw errors.
Practice your basic coding skills on the command-line. One nice place to do this is CodingBat where you get no syntax highlighting, no bracket matching, no red underlines, nothing. Don't forget to also practice those java and javac command-line skills too, though! (And any others appropriate to your workflow - for me, this would also include hg and ant)
Lastly, don't worry about it too much. It's unlikely you'll ever have to do a large piece of work without either NetBeans or Eclipse, so as long as you are capable of coding without them, and understand what the IDE is doing for you, it doesn't matter that you're slower or make more mistakes without it.