The critique of pure something or other

My 24-year-old son asked me to read a short story he'd written and render my opinion on it.
If you're like me, you know this is going to be trouble. It's been my experience that when people you love ask you to render a critique on something, that person wants to be reassured that whatever it is is wonderful.
"Now be honest,'' they say, and they are lying.
I read the story, an absurdist/surrealist little story that would give Ionesco a headache, would make David Lynch scratch his head and say, "I don't get it.''
The story involves a premonition of nuclear war, actual nuclear war, a lightning strike, a coup d'etat at a greasy spoon diner and a strange little girl selling cookies door-to-door.
"So, what did you think?'' Josh asked.
Once more into the breach, I thought, and decided just to jump in, saying that people in short stories ought to act like real people, you ought to be able to identify somehow with the protagaonist and I was lost.
Turns out there's a lot of symbolism in the story, and that it's about the impatience of youth, the immatuity of young nations and a critique of both Marxism and Bush's foreign policy.
"Oh,'' I said.
But we plowed through the story together and discovered the real theme of the story seemed to be the question of the philosophical equivalence of natural disasters and manmade catastrophes, I think.
"Maybe you should have thrown in a mysterious femme fatale or puppies,'' I said. "People like puppies.''
He's working on a second draft now.
How honest are we expected to be in our criticism of stuff like this?
I learned a long time ago that if your wife asks how you like a new dish she's whipped up and you don't care for it, you should say so, lest you wind up with a steady diet of green bean and prune whip casserole.
But this seems different somehow. Is it?