1) Special ad positions with front-page placement (currently #22 is "Willing (YC S15) Is Hiring a UI / UX Designer" https://willing.com/designer , a privileged post that can't be voted or commented on)

2) The moderators can and sometimes do intervene by removing certain comments that are critical of YC companies.

Comments make the forum more interesting to the community, which increases eyeballs and makes the front page spots more valuable. And shaping the discourse helps with damage control when necessary.