Right before the Promised Day transmutation, Father goes through his sacrifices talking about how poetically just Truth is in its punishments. Ed, who’d only wanted to regain his bearings and family, had his leg taken as well as his last remaining family member. Al, who wanted the warmth of his mother’s touch, had his body taken. Izumi, who’d wanted to see her child again, had her reproductive organs taken. Roy, who’d had his sights set on the top in order to reform Amestris, had his eyes taken. And Father doesn’t talk about Hohenheim, but following this line of logic, Hohenheim had wanted knowledge from Father, and gained it at the expense of everyone he’d ever held dear.
Ed rejects this Truth on the principle that Roy hadn’t opened the portal of his own volition so it’s senseless to say he deserved punishment. But it goes deeper.
Earlier on, Ed told Envy he understands–Envy is jealous, because humans have loved ones who are always there to pick them up, to bring them back, to pull them through, to support each other unequivocally. And this breaks Envy. When Roy tells Wrath the same, Wrath can only respond with how infuriating it is. Pride and Greed, at other moments, are shaken when a human suggests there’s value in the love and support of another person. Ling berates Greed about forsaking his human friends. Al challenges Pride’s relationship with Mrs. Bradley, and Ed challenges the lack of love and care he receives from Father.
And they’re right to be shaken, because THAT’S what disproves Father’s interpretation of Truth. Yes, Ed lost his leg, but Winry gave it back. Al had his whole being taken, but Ed cared enough to pull him out. And eventually, got Al’s true body back too. Izumi couldn’t have kids, but she got to raise the Elrics. Roy lost his sight, but Riza became his eyes, and Marcoh healed him. And he was restored so quickly because, as Ed pointed out, it WASN’T just for Roy to be punished as they had been. Hohenheim suffered under immortality watching all those around him die, but in the end he got to die loved, with family to succeed him.
Truth punishes. Father was right about that. But Truth is fair. Truth gives the chance to fight back. Truth lets people atone, and pull through, and get back up, through the aid of those who love them. Truth understands human nature, and lets people find absolution through genuine selfless love. Truth was THRILLED that Ed would give up his door to rescue Alphonse. “That’s it! That’s the right answer! You’ve won! Take him home!” Because Ed revoked pride and arrogance and selfishness and chose love, humanity, family. It absolved him, absolved Al. That is Truth.
And the completeness of this Truth, that there’s room for redemption and value in humanity and strength in caring for others, that it’s not just a force to punish humans foolish enough to strive for things beyond possibility, that’s what scared the homunculi more than anything.