If the whole purpose of a fruit/vegetable is to spread seeds by being eaten and what out, why are chilly peppers doing there best to prevent this?

Chilies have a very good reason to make themselves hot – protection.

The leading cause of seed mortality in wild chilli plants is a fungus called Fusarium. The fungus invades the fruits through wounds made by insects and destroys the seeds before they can be eaten and dispersed.

Capsaicin, the chemical that makes the peppers hot, drastically slows microbial growth and protects the fruit from Fusarium. And while capsaicin deters local mammals, such as foxes and raccoons, from consuming the chilies, birds don’t have the physiological machinery to detect the spicy chemical and continue to eat the peppers and disperse seeds.

Fun fact: Capsaicin doesn’t just help the plants that produce it, either. The consumption of chilies can help protect humans from the dangerous diseases that are so plentiful in tropical climates.

source: https://www.eurekalert.org/pub_releases/2008-08/uof-nrr081108.php

Capsaicin tastes like burning to mammals, but not to birds. Fruits that contain it are essentially reserved for animals (birds) that can carry it farther away, instead of being eaten by ones (squirrels, deer) that will eat it on the spot or nearby. That way, the plant’s seeds get spread more widely, and the offspring that grow don’t have to compete with one another as much.

Chilli peppers are bad for mammals, but not birds and birds can spread the seeds further than mammals. Capsaicinoids bind to the TRPV1 receptor in mammals to simulate the body’s response to overheating, resulting in sweating and other cooling attempts. However because birds don’t have the TRPV1 protein they are generally immune from the effects of capsaicin. – https://youtu.be/DbluR1DhTSQ

That heat sensation your mouth generates when eating a chili pepper is something only mammals like us have. Birds don’t even notice. To them its just a normal ‘fruit’ they can eat like any other.

The chili isn’t saying “I never want any animals to eat this”. It’s playing favorites by saying “I only want this to be eaten by the animals that will fly and spread the seeds really really far away from me. Go away, you pathetic mammals with your hair and your mammary glands, and, more importantly your lack of wings. This isn’t FOR you. Yes, Bats, I can hear you screeching, ‘not all mammals’. Look, this was the best I could do, alright? I don’t have eyes or a sophisticated friend or foe identification, so this is the best I can do. It’ll have to be just simply no to mammals, yes to birds.”

Then along comes humans who are a very weird kind of mammal that likes the pain and calls it “spicy”. Every signal in their body is telling them, “This is probably hurting you”, but since they don’t just operate on instinct they can tell that sensation is a false positive when the evidence shows it’s not actually harming them. And the chili plant is like, “well dang there goes that tactic”, but then it turns out that these humans will willingly plant more of them *on purposejust to get more of that food they make, so this also becomes a helpful survival tactic. It ends up being a different type of “I bribe you with food so you will accidentally cultivate my seeds” than was originally used on the birds. Now it’s become “I bribe you with pain so you will work for me and cultivate my seeds. That’s right humans, feel my pain. I know you love it.. Yeah you can’t get enough of it. Plant my seeds and maybe you’ll get a bit more of that sweet pain you seem to like for some oddball reason.”

Okay, maybe that’s a little NSFW for explaining like you were five.

Birds aren’t affected by capscasin. The plant wants to be selective about what animals spread its seeds. The seeds of chilies are small and evolved to survive long enough to pass through a bird gut, but not a large mammal.