There are three reasons.
The first reason is instructional.
There is a tendency among new users to treat Stack Overflow as if it were just another forum. However, the Q&A format here and the expectations surrounding it have some fundamental differences from forums. In that context, there is a tendency to (ab)use the comments feature for extended discussion, something Stack Overflow tries to discourage. The purpose, then, in limiting comments is to first give a new user time to understand how the site is different and what the expectations are for their commenting behavior.
The second reason is moderation
Site users can self-moderate a lot of what is done in questions and answers. They cannot as easily self moderate comments. That requires bringing in a designated mod (though flags), and on a site the size of Stack Overflow this doesn't scale well. Since new users are less trusted, we need to make sure they are contributing at first in ways that can be more easily moderated by high-rep users vs diamond-mods.
The third reason is to reduce abuse.
Note that you can always comment on your own answers, your own questions, and any answers to your own questions. Comments are also voted on differently than questions and answers, and don't affect your reputation.
With that in mind, comments could provide an easy avenue for abusive behavior among users. Someone does something you don't like? Just fake a new account and abuse them with comments from it. Your reputation score is immune, and your name isn't attached, so it's (nearly) consequence free. Limiting comments makes this harder, and means that you have at least one account that you're likely to care about (even if just a little bit), in case mods need to suspend you for bad behavior.