†testable hypothesis, data requested
Another hypothesis is that those are two largely disjoint populations on HN. With the smaller one displeased with the article and is likely to express that in comments. The other, larger one is pleased with the article and doesn't bother much with comments.
First of all... what difference does it make?
Beyond that, I's say "it's impossible to know". Upvotes don't have strictly defined semantics on HN. And they also serve as a defacto "bookmark" mechanis. Given both of those factors, it's hard to justify assuming any correlation between "support for the content of the article" and the number of upvotes. Some people are signifying "This headline caught my eye, I want to save it to read later", some are endorsing the content, other don't endorse the content but are voting in favor of the resulting discussion, etc., etc.
Is it that people think the comments are worth reading so much that they upvote the article in the hope that other readers will read the comments?
Very possibly. Seems like a perfectly reasonable scenario to me.
Are people afraid of flagging articles?
Why would somebody flag this? It's not off-topic or spam. Just because you think a cheat-sheet isn't a great idea, is hardly a good reason to flag the post. But, then again, flagging also doesn't have particularly well-defined semantics either. :-(
There's no reason to assume they are the same parties.