I used to find the starter putter was ok from 20ft and less. However, anything over that and, like you say, the ball had a mind of it's own and often defied the laws of physics. Starter equipment is designed to get you hooked on the game, and it does that so majestically - just have a look at how long some people have been here. As Piz says, when you upgrade your clubs things get better, but even then you won't have 100% accuracy.
If you play real life golf I'm sure you will appreciate that you don't always hit all your putts on the line that you intended, even if you feel you hit it sweet (i.e. the equivalent of a ding'd shot on WGT). And so the makers of this game have tried to replicate that by allowing each club precision and forgiveness. Admittedly, in real life golf it's not so much the club that's at fault, but more the person holding the club, but I personally think they have done a damn good job in a way that is fair-ish (could definitely be improved), and the players who can cope with the deviations the best are those that take the top spots. I'm not one of those players by the way!