Chalk it up to different preferences. I prefer Vundle too, never could get Pathogen to work, but Vundle just does for me. But others were using Pathogen before Vundle appeared and have no reason to switch.
Everyone used Pathogen before Vundle, as Pathogen is older.
However after an extensive use of Vundle, it's the fastest way to deploy your environment from scratch - or to add, modify or delete a plugin. I really don't troll here - but honestly, managing plugins with Vundle is such a joy that I don't see why a company like Square releases a Vim project using Pathogen. And I'd looveeeee to know the reasons - is it indeed because of personal preferences or is there something I'm missing?
It's literally copy and paste. I understand preferences and taste, but you make it sound like you need a degree in particle physics to make the thing work...
I know, and back when I tried it, which was probably years ago, the problem was .vimrc line execute pathogen#infect() always errored out. Couldn't figure out why at the time, then found Vundle, it worked perfectly, been using it since.