I'm sorry but I still agree with your notion that Mr. Threehorn is a jerk. I view him as a more complicated character, even insecure. In LBT 5, I believe it was, he wanted to blame Littlefoot for the children going missing, but when LF's grandpa questioned him on this, Mr. Threehorn said he had to blame somebody, and as he said that, he seemed hesitant, reluctant, even regretful. This, to me, is a sign of insecurity.
As for why he would think we were "up to no good" as you say, you have to think about where Mr. Threehorn grew up. He grew up in the Mysterious Beyond, where predators were free to attack, and there was no valley wall protection. Out there, especially after the plants died off and the migration occured, it likely paid to be suspicious and cautious about pretty much anything that he didn't know. Mr. Threehorn's "I'm suspicious of this/distrustful of that" attitude was likely a smart way of thinking.
I can understand Mr. Threehorn's perspective. He doesn't really wish harm on anyone, not even Littlefoot, whom he isn't overly fond of. I just think Mr. Threehorn is so used to living like he did in the Mysterious Beyond that he just hasn't learned to adjust to the Great Valley. He probably thinks being cautious and skeptical about any strange thing is the best route to go, and I partially agree with him. You never know what is bad, what is good, who can be trusted, who can't be trusted.
If you still think he's a jerk, that's fine. But I don't agree with you.