1. Make every note positive.
By positive, I don't mean tell people things are good when they're not. I mean phrase the note in a positive way.
Every negative note can be phrased positively, using a few more words.
"I have no idea who this character is." -> "I'd like to see this character defined more clearly."
"This is confusing." -> "Can you clarify what is going on here?"
"This is a gaping plothole." -> "Can you come up with a more convincing way to get here?"
"I don't believe this twist." -> "I'd like you to work a bit harder at earning this plot point."
2. Note how some of these notes are phrased personally. "I feel..." "I'd like..." It helps to avoid the Voice of God in notes. They won't be any less authoritative. Anything you say will have exactly the same amount of authority whether you claim it's the facts or your opinion. But if you state it personally, it acknowledges that you could be wrong. And you could be.
3. Note how some of these notes are phrased as a question. "This is confusing" provokes the reaction, "No, it's not! You're just an idiot! Screw you! I'm going to throw myself out the window now." "Can you clarify this" provokes the reaction, "Yeah, sure, sorry 'bout that. I'll get right on it."
Obviously it's important to be clear, and smart, in your notes. But when you have a choice between phrasing a note as "this is bad" and "I'd like to see this improved," the latter is almost certainly going to allow your note-taker to focus more on your note, and less on that peculiar combination of anger, guilt, humiliation and nausea that is every writer's instinctive reaction to criticism.