In addition to the above excellent answers, I'll just add that the Dock is meant to be a convenient launchpoint for the apps YOU use the most. Apple put a few suggestions in there, but you should customize the Dock to work the way YOU want to use it. I recommend maybe 12 or so top-used apps be dragged into it from the Applications folder (as explained above, they're just links, so the apps will stay in the Applications folder). Customize it for your needs.
In addition to that, I suggest you place the entire Applications folder in the Dock as well (remember to right-click on the icon and choose "Folder" so it looks like a folder and not a stack of icons). Your Home folder can go beside that as well, and the Downloads folder should already be there. Once click access to everything!