The problem here is that this was badly put together legislation. I don't think the idea of net neutrality was actually debated at all in reality. The need to abolish mobile data roaming charges in the EU was front and centre of the needs of these MEP's constituents minds and they would not vote this down, it would've been mad for them politically. Whoever wrote this piece of legislation is to blame here.
I would be very surprised if this didn't come back for debate in another form prior to it's adoption.