Generally speaking you should not do something the user is not expecting. Be that perform an action that wasn't expect when they hit a button (e.g., exit & save when I hit a button just labeled "save") or modify the formatting of a post I put in.
I wouldn't say it is harmful, but it would not be helpful either to auto-link "well known" sites.
For example, where will I go if I click on this 'Facebook' link:
I saw this great page on Facebook recently!
... but what about this one:
I saw this great page on Facebook recently!
... and finally:
I saw this great page on Facebook recently!
Looking at #2 & #3, what should the reader's expectations be for the links? What was the author's original intention, and did the auto-parser change it?
Auto-linking direct link (e.g., http://www.facebook.com) is common, and generally useful as it would save a highlight/copy/paste. StackExchange does it, and in the image below you can see that vBulletin (a popular form software) does it too:

But is also gives the author the ability to turn it off, as the intention in the post may not be to have them linked.
Thankfully the auto-parsing of smiley faces is unchecked by default, so my in-line :) is not auto-parsed to a horrible img
which I did not intend.
Assuming user (or author) intent can lead to a poor user experience. In this specific case the potential annoyance is small, but when results do not match intentions things can get messy in many situations.