One of the things I've noticed is that some people get downvoted for bike shed reasons; if you're making an opaque technical point, your comment's score will sometimes be more indicative of its politeness (which everyone feels competent at assessing) rather than your comment's correctness (which only a few feel competent at assessing).

On a similar note, the established voting pattern in a thread that you join matters a lot---people establish 'sides'. If you are willing to rebut particular arguments from the side that is already winning socially, expect downvotes regardless of merit (even if the comment on net ends up positive there will still be some downvotes according to existing trend.)