I suspect I was the guilty party.
I treat flags as having a sense of urgency. And toward that end, I welcome the flags for spam or for the rare cases of members starting verbal brawls. Bad questions should be handled via close votes (I know, the 3K issue) or Down Votes.
MrChrister's answer supports this view. Else, I'd invite him and John to discuss how to align our styles a bit better.
I'll share this - as a mod, I no longer have a "vote to close" option. My vote is a hard close. I tend to err on the side of caution, and would prefer not to be the first, and therefore only, vote closing. I also think the question you cited has a small window of time where a comment or answer might help the user before the question is closed.
In the end, I think my flag rejection was "useful" and the question was closed soon after.