I don't understand this either.
Although the few families that I know who have done this have usually then called the son by the middle name, which again I find a bit hard to understand because it makes more sense to me to use the middle name to honour someone else with if the person being honoured is still alive and give the baby it's own first name.
And I say this as someone who named my LO after my grandad, but my grandad has passed away and so isn't hear for the names to cause confusion, which makes it alright (to me).
My DH though, has his father's name as his middle name and he wanted LO to have it as a middle name too. It's a fairly popular name that I do not like, and it's been mentioned on this thread so I can't share it, but thankfully DH's brother had used it for his eldest sons middle name and so I managed to convince DH it was 'taken' 
So then he wanted to use his own first name as a middle name, but that would have meant an unfortunate set of initials, even if we had tried to find a further middle name for LO, so I refused to consider it. DH threw a bit of a strop and I insisted that since LO was getting DH's last name it was only fair to go double-barrelled with my maiden name, to avoid the terrible initials and get a bit of me in there somewhere.
DH hated that idea so the argument was resolved and LO has a perfectly ordinary set of names and initials and no double-barrelled surname.
I suppose it's as someone else has said, each to their own.