--edit--
The length of this post got out of hand, I'm going through and embolding key points for folks who like things short and sweet.
I'll look into whether or not there's a modification to the system to show who the comments are from. I would be surprised if someone in the vBulletin community hadn't made such a hack yet.
The reputation system is a standard feature for this software. I believe it's also standard that users can opt to not display their reputation in their UserCP settings. Reputation goes a bit deeper than some dots on user postbits. With another reputation, a registered user can become a mod. A mod with enough reputation at some point becomes a senior mod. It's a built-in system of advancement designed to help keep the board in check and promote participation.
I think it would take a lot for someone to really get a lot of negative rep here. Abusing the system is almost impossible. Using Tibor as an example, sure, there are a number of people who probably give him negative rep every other post. But the system is smart about it. If it sees the same people dinging him over and over, their input towards his rep becomes less of an impact every single time. After a few times, someone making a mission to blast you will have zero ability to swing your reputation one way or another, and even across the board the efficacy of their reptuation votes diminish at the same time. It's designed to learn who abusers are and take their voice away within the system. The points you give or take when you apply reputation are not a fixed amount. How long you've been here, how many times you've posted, and what your own reputation is all factor in to how many points you can give and take. Even how you handle rep is taken into consideration. If you're always positive or negative, the power of your 'vote' weakens. If there's some balance to it, the power increases. But getting back to my Tibor example, while there are people who will ding him, there are also people who will give him positive reputation as well. If there are people who disagree with you, there will be some that agree, no matter your point.
The only downside I see to making rep author comments public, is that it could chill the system somewhat. People might not be as willing to really tell you what they're thinking about you if they know they're going to get blasted for it.
Rep that has affected you negatively will show up in UserCP with a red dot, positively with a green, and then some with show up grey. That just means that the person giving or taking rep didn't have enough juice to sway your value one way or another.
Bottom line is that if you have some sort of personal issue with the system, ignore it.
I'm also all for people opting to include their usernames in rep comments. I often at least leave something suggestive of who I am. The system being there doesn't change people's perspectives. If anything, it gives you a chance to hear (for better or worse) what someone's take on you might be. We're all going to get sophomoric dings for various comments we make, but over time, those get washed out by a broader message.
So here I sit at the end of this reply, wondering if making the names of rep givers and takers public would be a good thing at all. If someone wants to pat you on the back or backhand you, they can do it in the thread.
--edit--
Okay, here's where we are. The option to disable reputation was not enabled by default. It now has been set that way. Which for some reason means that some people are enabled, and others are disabled.
The option to change it either way can be found in your UserCP (link above this point on the red navbar, far left). Once in there, look to the navigation on the left side of the screen, and find User Options. Within the first area or two, you will see a box that you can check or uncheck to toggle the reputation system on or off.
I was reading through reputation comments I have received recently, some were positive, some were negative, some didn't adjust my rating at all. A few people left indications of who they were, others didn't. Overall I see value in such a system. It allows someone to agree without having to trumpet as much in a thread, or disagree without getting into a huge debate about it. I think 90% of the time, if someone disagrees with you, you're going to hear about it in the thread itself. The other 10%, if they don't feel like they can or want to argue the issue and just ding you instead, then so be it.
NO ONE sees your reputation comments but you. Even as admin I can not go into your account and see what people have said. So this isn't a system that just allows people another route to slam others. Ignore the stupid comments, and just focus on the constructive (if you use the system), that's all I can really advise.