This is the answer I give every time these kind of "player X from a past era had Y stats and didn't win!", and it applies here as well.

MVP voters used to stress the value part of that award. There was much less stress put on the raw stats and someone like Gwynn who scored substantially fewer runs / had less RBIs than the other contenders just flat out didn't contribute as much 'value' to his team. If you get on base every single time and just get stranded there are you really helping your team win? Or are you just padding your personal stats? By today's standards, and the reason we have metrics like WAR, fucking obviously you are still contributing even if you do not get driven in.. but no value given towards a win meant less consideration for the MVP back then (with exceptions, obviously).