The Ellipse and Rectangle tools create a different kind of objects called "shapes". (Also Star and Spiral tools create shapes.) They aren't paths, and don't have nodes, so they can't be edited like paths. But they can be easily converted to paths, using Path menu > Object to Path.
Confusingly, path operations (union, difference, etc.) (including Cut Path) CAN be used directly on shapes, even though they aren't paths. I guess it's just an exception to the rule. But otherwise the shapes need to be converted to path, to edit the nodes.
There are other kinds of objects too. For example, Groups and Clones. With the Selection tool enabled, the status bar will always tell you what kind of object is selected.
However (more confusing info) you can't use Object to Path on Groups or Clones. For clones, you have to break their link to their parent. For Groups, there are a few options. You could Ungroup. Or there's a way to "enter the group" where you can work on individual parts of the.group. But if you use the Node tool, and click on a path that happens to be in a group, you can still work on it with the Node tool, without ungrouping.
When I first started learning Inkscape, I found Help menu > Tutorials to be extremely helpful. Especially I would suggest "Basic", "Shapes", and "Advanced", for beginners. Even though it's called "Advanced" it really covers very basic info. "Elements of Design" and "Tips and Tricks" are also good for general info, but perhaps are somewhat advanced. All the others are for specific techniques (as opposed to general info).
Whoops, you guys both posted while I was typing

Edit
Speaking of manuals, I've always thought this one was good for beginners:
http://www.microugly.com/inkscape-quickguide/