Etiquette for effective workshop comments
I am not sure that your questions at a conference are necessarily a major concern. If you look at how science is propagated, conferences are typically a step before publication. Therefore, it is noble of you to think of it as a point where you can provide constructive comments to authors about their work. However, the most critical point comes when work is published and peer-reviewed.

Based on your experience at conferences (which I to some extent share) you can ask yourself the following: Is the author/presenter interested in your comments. If he/she is, then it would be counter productive to ignore your questions. The question-and-answer format, on the other hand, is too brief and fragmented considering the time constraints of a presentation schedule to be the forum for constructive criticism. That is probably also why the more aggressive questions dominate. In the end, there is nothing wrong with approaching a person during a break to initiate a deeper discussion. you will then also get a better feeling if your comments are welcome.

A final thought. I tend to think as the saying: it is sometimes better to be silent and seem a fool than to speak and prove it. You can exchange "fool" by whatever trait you wish.