In substance I agree with you. But at the same time I think HN would be better off without downvoting at all. An ethos of free speech is entirely lacking.
I don't know why you would expect an ethos of free speech from a privately-owned, privately funded service provided to you at-will by venture capital. YC isn't a charity organization.
I think you're right, not essentially because YC is a privately-funded service, but because their sense is that the majority of their users enjoy expressing their disapproval of those with whom they disagree.
The fundamental reason why you're not entitled to free speech is because HN is not public property. You can manufacture whatever kind of persecution complex you want, I don't care.
On the contrary: we know, from the paradox of tolerance, that some speech must not be tolerated. That's philosophy, but real world experience backs it up. The parable of the Nazi bar has roots in the world, and we have the example of the heat death of Usenet as well