It does not penalize the article, as even before this concept was given a name it was already clear. The only people it "penalizes" are the people who have to see the comment every single time an article, no matter what the quality level of the content, happens to have such a question-marked title. Think about it this way: the article got voted to some place, and maybe is even on the front page; do you think yelling "Bettridge's law of headlines says 'no'" is changing that vote?
Do you think people reading the comments are going "ah, that is something I had yet to consider about this article; I had previously been curious to know the answer to this deep and burning question, but now that I read this comment, it is clear time that not only am I a fool, but I should down vote this article, all articles like it, and start my own crusade to scream the name of this wonderful law of headlines every time I see such an article".
The best you are getting is "oh, I didn't realize someone had assigned this a funny 'law'... that will be a great trivia item I can being up to demonstrate my epic knowledge of jargon". The result is then just another person in the article comments adding noise. It is nothing more than a way to add mild justification to the seemingly-dying practice of yelling "first": you just need to know, for each article, what bingo terms happen to apply, and then be he first to lay claim to them.
This is valid in the same way that it is valid to point out when a headline contains a false and self-serving claim.
I don't think anybody is under the slightest illusion that having heard of Betteridge's law demonstrates any particular intelligence.