"It is good."
Translation:Ĝi estas bona.
Estas bone is correct when you're talking about general statements, say you just wanted to shout out "wonderful!".
You would then say: "Mirinde!"
Thus every time it is just a general statement, like estas bone, which means something is good, not a specific it like a dog or a train, but it's just a general statement and thus -e is used.
When you're talking about a specific it like in this sentence, maybe it's a dog or a bicycle or something, then you use the adjective ending -a to describe it, as adjectives go with nouns.