The people who named it no doubt put much more thought into the name than we are, and I am confident they knew the implications of the word 'uber'; also, emember that it was founded by Travis Kalanick whose public actions seem to fit some of those implications.
Also compare the word 'uber', however you interpret it, with words like 'google', 'yahoo', 'GNU', 'quark', 'charmed', 'C', 'C++', etc. Those have wit, humor, and disarm ego. (In fairess, maybe there are similarly witty names now that I'm not thinking of?)