yeah, that’s the way it is setup. it is a bit less orderly than the pdf, but quite a bit more free. 
the first page of the manual is “index.html”. Just open it in Firefox or the like.
btw, I should mention that when I re-learned Blender 4 years ago, I used the 2.3 manual, and it was out-dated then. there are several times in the manual when it will tell you to look for a certain button in the edit panel or something, but the button is not in that place anymore. Yet another reason that I recommend the more up-to-date manual on the blender wiki: http://wiki.blender.org/index.php/Doc:Manual
Have fun either way 