Presumably because the comments are mostly spam or other noise? If they cleaned that up, more people would read the comments, maybe?
Also, a large part of it may be that the comments are at the bottom and a large part of their readership don't get that far on many articles. Some will read the headline & byline, some complete the opening paragraphs, and only then if it seems interesting enough (or they are otherwise lacking anything to do) will people read on further (never mind all the way to the end of a long article). Getting around that by putting the comments higher up probably isn't a good answer. I've seen some places have a "<number> comments below" link near the top but I can't imagine that drawing people through unless they would read that far anyway or the <number> is high enough to suggest some interesting controversy.