Let's imagine the following situation: someone was once a soldier on a mission (is not anymore!) and wants to write about that period of time. He wants to talk about the feelings of the locals in the mission's country. However, despite writing about the particular people at a particular period of time, he actually wants to primarily address the feelings of locals towards soldiers in general.
"I (have/had) always wondered what people really think/thought about us. Do/did they hate us or do/did they appreciate us?" (please note that the word "always" is meant to indicate it was so during the entire time of the mission.)
So, one might say he actually still wonders about that (both what the natives thought about them at the relevant time, and what they think about soldiers nowadays), but he is no longer a soldier (so "have wondered" probably won't work). I think the "do" version sounds much better, but I'm not sure whether its's entirely correct.