There are basically three ways you can lose 100 rep:
- Offer a bounty on a question
- Have some piece(s) of content you posted within the last 90 days that has votes adding up to 100 rep (10 for answers, 20 for questions) deleted
- Get docked for offensive content
If its not reason 1 or 2, then it must be reason 3.
Offensive content is judged by anyone on the site flagging a post as such (comment flags don't count for this), and either enough other members (5, I believe) or a moderator agreeing with the flag. At that point you will see the content is marked as deleted "by community" and you will receive a 100 rep point penalty.
In my estimation this is a pretty fair system to incentivize good manners. Most rep changes are weighted in the up direction with even 1 upvote out-weighing up to 5 downvotes but there are consequences if you cannot keep your self in line and your content respectful.
Edit 4: Removed edits 1 through 3. I stand by my first assessment above, but after that I got distracted and the subsequent edits could be classified as "feeding the trolls". On review I have decided even meta is better off without that mess. The morbidly curious may review the revision history to see I am not trying to hide even my own mistake, only spare others the mess.