What if you are seeing an interesting (or not) question and want to answer it, and if you can't understand something in the post, because you don't know it, for an example consider a question regarding hybridization (like $\rm sp^3d^2$) and you don't know what is d (orbital). In that case would you down-vote it as "unclear" or try to study that either on internet or in your course or waiting for it to be taught to you until the time comes? Your opinions.
Asking for clarification is one of the main purposes of comments on Stack Exchange.
A clear question is absolutely necessary to get a clear answer, and in the case that you are speaking about, it was merely an issue of notation, not about ignorance of the subject matter at hand.
Voting is anonymous, and as such, you have no way of determining whether someone making the comment has actually downvoted your question. As to the general case, people can certainly downvote if something is unclear, as the mouseover on the downvote arrow indicates.