The main reason for not knowing where to start with a tool like Hammer or Radiant (Radiant is basically the same sort of tool as Hammer but for Quake 3, Wolf: ET etc.) is not knowing what the principles of construction are. This is a shame because it's actually pretty easy.
It's like building with Lego.
You use the block tool to make 'brushes' which are literally 3D building blocks used to make up the world. You drag their shapes out with the mouse and move them around in the viewports to get them in the right place in the world. A simple room has a block for each wall, one for the floor, and one for the ceiling. They all meet at the corners so with no gaps so that the map can be compiled correctly. Even if there's sky up there it's just a brush with a special texture on it that tells the engine to draw the skybox in that space.
If that makes sense you should probably go work through the first map stuff on Valve's developer site.
Work through what each page is saying in Hammer while you're reading, don't move on until you're happy you understand, and don't be afraid of going back when you've forgotten how to do something - not everything will stick first time. After a while things will start to make sense quicker.
There are sample maps included in the SDK, once you have an idea of how you navigate maps in Hammer and how to create stuff, you can look at those to see how this stuff all fits together. It will all look pretty baffling and complicated at first because there's so much stuff in them but bear in mind the stuff in those maps has been built up gradually in a number of stages, each of which is quite straightforward.
Don't be deterred if the first things you make look like ass, almost everyone ends up making a few clunkers as they get the hang of things.