Of course you'd rep posts you agree with. I sincerely doubt anyone is going to rep something they disagreed with. "Hey, your logic is faulty, you've ignored important facts and your general philosophy on this issue is 100% wrong ... so here's some rep!" Not going to happen. It was a rep system, not a congeniality recognition system.
If somebody made a persuasive case or had a particularly interesting take or wrote something well, that got rep. Nobody who had a high rep thought they were popular (except Raisor, who knew he was popular), just that people liked various thing they had written/posted. Neg rep was a tiny sliver of the pie.
The upside of the system is that if you posted something you thought was brilliant and it landed like a dud, the zero rep you got for that post would sort of clue you in on that. The biggest problem post-rep, IMO, has been the influx of "nobody cares" posts. Clearly some folks think their personal borefest has some sort of constituency. I can guarantee you that if we had a rep system they'd be disabused of that notion.
I'm hopeful the new system will give rise to more interesting people posting here. The board needs it.