Who was throwing rocks at his tent? Or vandalizing it so he has to scrub the paint off?
Let's get to the bottom of this mystery once and for all! Breaking down the NPCs by likelihood:
The "Definitely Nots": Gus (Obviously cares about Linus), George and Evelyn (Obvious reasons that don't bear elaboration), Birdie, Bouncer, Governor, Grandpa, Professor Snail, Leo, Kent, Sandy, Henchman (No opportunity), the Wizard (friends with Linus).
The "Probably Nots": Mr. Qi (doesn't live nearby to say the least but has mysterious power so not impossible), Elliott and Willy (lives halfway across the world and they have compatible philosophical viewpoints to Linus), Emily (she's all about folks being accepting of others), Harvey (He's the town doctor and all about watching out for the community), Haley (the idea of her interrupting her beauty sleep and picking up a rock is laughable)
The "Unlikely Suspects": Jodi, Marnie, Leah, Clint, Gunther, (No real reason to suspect them and they're far away, but no reason other than distance to rule them out either), Krobus (we know he occasionally sneaks around in the dark but doing things to draw attention seems unlikely), Penny, Caroline (They're close and have some opportunity, and both have a degree of home strife, but I just personally don't see it based on personality, might be underestimating them though)
The "Maybes": Lewis (Linus isn't exactly a selling point for the town and doesn't pay taxes, Lewis barely ever acknowledges him. Clearly they're not friends), Shane and Morris (they're both jerks, and thus it wouldn't be out of character), Pam (she drinks a lot, could do it while intoxicated), Sam and Vincent (home troubles could lead them to act out but they're far away) Jas (similar but she's even further away), Alex (he's an athlete so throwing rocks is in character and says and does nothing to rule it out), Pierre (might have a beef with Linus because he doesn't shop at his store)
The "Likely Suspects": Sebastian, Robin, Demetrius, Gil, Marlon (they definitely have opportunity and could have some beef, legitimate or not, with Linus that they just don't talk about with you, and Robin certainly has ready access to stone), Maru (the same but for her it might not even be deliberate, could be the results of experiments gone awry), Abigail (she goes to the mines and fancies herself an adventurer, might have tried to 'practice' on Linus)
My "Best Guess": I actually think it's not a human doing it. The most likely to me is the Dwarf. We know from the cutscene with Krobus he has militaristic tendancies and gets around. We know he neither understands nor respects human values, including but not limited to personal property. He's incredibly close by, and is naturally suspicious of others.
The "Unexpected Plot Twist": Linus. Could be making it up, could be sabotaging his own tent, who knows? He could have dreamt it, he could be crazy, lots of explanations don't necessarily involve his tent being targeted and sabotaged by someone else. After all he says how he wouldn't be welcome at a lot of things but literally no one has a bad word to say about him or indicates his presence is ever unwelcome. Not saying it's likely, but it's certainly possible.