You're right that fenders won't stop the rain coming down on you from soaking parts that don't want to be soaked. But I have found fenders to be surprisingly effective at helping to keep me dry and my bike clean. Before I had them I would dread getting caught in the rain because me and the bike would end up covered in wet limestone sand from the rails-to-trails I ride. But with the fenders, that just doesn't happen anymore.

Then, with a Gore-Tex shell and Gore-Tex shoes the only parts that get wet are my head and my thighs. And, generally, neither one of those bother me much (but I might feel differently if I were in rain all day).

When I was thinking about them I asked the manager at my LBS who races and also commutes -- and does all types of riding and so tends to be open and pragmatic: He said:

Do you know what they call fenders?
... No, What?
Common sense

I have a road bike that I use on nice sunny dry days and a utilitarian hybrid with fenders and disk brakes if lt looks like rain.