Are any of the characters in the main timeline of Aeneis (or Aeneid) historical, that is, known or strongly believed to have really existed? I want to exclude prophecies of later eras in Roman history. I assume most characters are either from the traditional Roman myths or were created by the author.
There is a possibility that Dido was a historical character. Quite a lengthy discussion can be found in the Wikipedia article on her - https://en.m.wikipedia.org/wiki/Dido. But if she did exist, it may well have been in the late 9th century BC: that is when Carthage is thought to have been founded. If that date is right, and if Dido was a historical personage, then she lived several centuries after the supposed time of the Trojan War and of Aeneas.
If Dido was historical and lived in the 9th century - as some experts and ancient authorities think - what happened was that at some point in the centuries after her death someone decided that it would enhance the Aeneas story to link him with her. Whenever this was done, people were not too bothered about the chronological discrepancy - again postulating that Dido was historical. There is a possibility that the link was made before 200 BC - a fragment of poetry by Naevius (who died in 201 BC) may be part of a conversation between Dido and Aeneas.
I think most experts agree that Carthage was founded in the late 9th century BC, and if that is right, and if the Trojan War is placed early in the 12th century BC, there is no escaping the timing discrepancy. Also, according to Plutarch (his life of Romulus) some Roman authors held that Aeneas was only a generation or two before Romulus and Remus who are said to have founded Rome in 753 BC: were that the case, Aeneas could then have reached Carthage in the late 9th century BC, soon after it was founded, but this merely creates another dating problem given the generally supposed date of the Trojan War. Ancient writers, though, differ considerably about when Carthage was founded: some concur with most modern experts, and suggest the late 9th century BC; others suggest an earlier date, possibly as early as the late 13th century BC, which would eliminate the timing problem.
Remember, myths are not facts, and they develop and change over time, and mythological time is not the same as chronological time, and is much vaguer. In the legends attaching in medieval times to Charlemagne, Alexander the Great and King Arthur, elements were added over time to the legends some of which would have been chronologically impossible from a historical perspective.
I think Virgil would not have been too bothered about any of this: he simply used the Dido/Aeneas story, however it came into being, as part of his material for a patriotic propaganda epic.