It's another way of "liking" the comment or voting it up. The user is essentially saying "I agree with this".

People sometimes flag such comments because:

1) The upvote mechanism was created for 'this' purpose.

2) These types of comments don't necessarily add much value to the threads and the community at large is very protective and self-governing in terms of maintaining the integrity of the site.

... Personally, I don't care. I'm sure I've 'this'd comments before in one form or another.