I originally thought this too, and I did have trouble getting my first 50 rep. (basically I browsed things for a week before I answered enough questions/asked enough to get 50 rep.)
But, that being said, if people with one rep could comment then that would mean anonymous first time users could. This is not good. Along with the extra spam and offensive/offtopic comments, new people may start seeing this as more of a discussion site with Q&A being the topic. This is definitely not wanted. The focus of SO should be questions and answers. Comments should only be there to get clarification on a question or answer. (or to add humor sometimes, or just plain make an offside comment).
I say it'd be safe to make the rep requirement as little as 10 or 5 or something, but letting anonymous new users comment immediately is bad because there are still way too many new people that think of this as some "biig aws0m3 m0d 0f phpbb"
And also more importantly, if I had been able to comment then I would have ended up giving a lot of answers as comments rather than answers. I still do this sometimes..