I think its more for the cleaner look, I use a blue line on my ball, and sometimes the sight of that bugs me on my approach shot, but it helps my putting so I'm not about to remove it.
It is ultimately your responsibility to make sure you are hitting your own ball. It doesn't matter if I am the only one in the fairway, I still take a look to make sure it is my ball, you can never be too sure!
The tournament I played in this past weekend, one of the pros incurred a 2 stroke penalty for hitting the wrong ball. It was a bad situation because there were spotters/markers marking the balls from the different holes and the marker told the guy that was his ball. He still should have looked and it is now a lesson learned, but kind of sucked that the marker told him it was his, and it ended up not being his.
I started putting a line above and below the brand of ball *titleist, wilson, callaway* and drawing a line either all the way or halfway around the ball through they alignment marking/model name as well. It makes it much easier to identify the ball regardless of it's orientation in the rough. Sometimes I vary a bit in the mark on/near the label but I almost always have the a line around the ball. The line is dual purpose, it's great for a quick reassurance that the ball is mine as well as helping me a little with lining up putts and tee shots. Ever since I started doing this I've not had any incidents of wrong ball being hit by myself or a playing partner.