I agree that an IDE can make things seem more complicated than they are/should be, but with the right guidance an IDE is fine.
If you take some time to read about the different parts of Eclipse or Netbeans, and how their UI's are laid out, you'll be fine, perhaps even better off than without using an IDE.
It won't be long before you'll encounter an error, or before you'll want to add a break to a line, enbaling you to step through every statement in your code - and that's much more complicated without an IDE, IMO.
The things you need to focus on from the beginning, regardless what IDE you'll be using, is (1) The code view (that main area that you can type into) like mainstream text editors, it allows a tab for every open source file.
(2) The project explorer (that bit showing your project, the contained packages and the source files as a tree structure)
(3) Basic project settings, where you can add some jars to extend your project with. This will be more important later on, but it's essential for setting up a project in the first go.
The rest will in my experience both as a TA and a developer come gradually.
Of course, for the very first steps it may be easier for some to go without an IDE, like Nercury says. Check Oracle's first lesson on the topic. But again, I wouldn't call it a gamebreaker if you start with an IDE.