There is this theory going around by "giveaway bloggers" that non-spammy comments can cause a Google penalty. You can read about it over here and over here - where you can see that an SEO told this site that they are penalized in Google because of the bad comments they have.
The SEO linked to Google's guidelines on user generated content and proof.
We've covered the topic often here including:
- Google's Take On User Generated Content & Quality
- User Generate Content Does Not Mean Spam
- Google: Comment Spam Can Hurt Your Site's Ranking
- Google's Publisher Quality Enforcer On User Generated Content & AdSense
So what is the real deal? Should you institute a policy like these "giveaway bloggers" did to remove any comment that is less than three words? Um, yea! I get tons of comments here and anyone who leaves a three word or less comment, 99% of the time, it is not adding any value. Those, "thank you for posting" comments are always about getting a link back to their sites. I do my best to delete those not because of Google, because they waste your time as a reader on my site.
Bottom line: If someone comes into your house and starts messing it up, would you let them stay? Depending on the quality of your home, your threshold for that will change. If people are messing up your blog, aren't you going to clean it up and kick them out?
Giveaway blogs, go ahead and take offense, are the lower quality homes. They are probably more likely to attract people who are less quality because of the nature of "giveaway." Why in the world would you want to read comments from others saying, "good post" or "thanks for posting?" If you let those types of comments on your site in mass, then it shows the type of blog you have.
Don't let outside people mess up your home - it isn't nice to those who live inside your home.
(Note: I expect a ton of "thank you" comments now, which I will spend most of the day removing).
There is such a thing of content spam, spam is spam, if you do not protect your site from spam (not just link spam), then Google will think your site is spam.
Update: I've asked Google's John Mueller about this and he said, generally the length of comments would have no barring on if a page would have a manual or algorithmic penalty. I'll post the video of this as soon as it is published.
Here is the video, my question starts at 28 minutes and 55 seconds into the video:
Forum discussion at Google Webmaster Help.