Hello Michael,
We use Masterpages for many of our applications and find them a benefit but I think your right to question how useful they are.
For our applications that have a large number of pages it's great to be able to extract a lot of the style information to one place. I know it's possible with include files etc but as Masterpages are the main method for Visual Studio it's obviously integrated very well and easy to use.
The biggest benefit for me is that I tend to use the same Masterpage across many applications thus giving them all the same look and feel. Again I know this can be achieved in other ways but it's Visual Studio integration makes it the easiest for us.
I think the best way for you to decide is to try them and try an alternative method as well. Pick your favorite and then let us all know!