In the first two stanzas, the boy questions God and Christianity. In the first, he doesn't see how he could know about or understand God, when all he has to work with are his lesser (compared to God) thoughts. In the second, the boy proposes that he should love all of God's creations equally, which all share the Earth with him. Thus, he cannot love the Priest more than a bird.
In the third stanza, the Priest grabs the boy, angry at his blasphemy. Questioning the faith is not looked upon favorably. But there's something else here too: the observers, the other members of the church, do not see the Priest as attacking the boy, but only as helping him. Even when the Priest uses physical force, nothing seems amiss to the faithful.
The fourth stanza is the money stanza. Here, the Priest declares the boy a fiend, and spells out his offense. His offense was using reason to examine and judge church doctrine. The Priest considers his doctrine a "holy mystery" which is not supposed to be explained or thought about rationally.
The final two stanzas describe the brutal punishment of the boy. It's not clear if he's literally burned to death, or only metaphorically. But it is clear that he is badly hurt, and that the church turns a blind eye to the boy's parents' tears. Also note that Albion is England.
The final line is a very powerful one. Everything up to this point tells a tragic story where the Priest is clearly wrong (I suppose this may not be so clear to everyone; feel free to discuss that in the comments). Phrasing the line as a question is very important. There are no accusations to deny. There are no claims to refute. There's nothing to argue with. There's just a question to ponder. Are such horrid things done in England? Certainly they have been. And certainly some people still trumpet faith over reason. Maybe they don't burn blasphemers any longer, but how different are the suppressions of reason in favour of faith that do take place?