that is a good point, I've gotten negative rep in this way before, and it is somewhat annoying, but I'm afraid that sometimes people deserve negative rep, and short of moderating all rep points awarded there is nothing really that can be done about it.
I have a problem with the rep system, in short it won't let me award rep points to some users as I have awarded rep points to them in the near past,
I can understand that it has to be that one person cannot rep their friends too much, but I'm in a rather strange position of awarding rep points to what I consider good answers to questions that I have not asked, it's a way of awarding those members who are helpful (and who are helping to build a strong community), (regardless of whether they are my 'friends' or not) however, there just plain doesn't seem to be enough of those people! hence there are a handful of users who should be getting a rep point for being helpful to others, (or just generally insightful) that just arn't getting rep points because (in my eyes) they've been just too good (i.e I've awarded them a rep point in the past).