Are any fundamental Protestant beliefs historically heretical?

One way to look at this question in an objective manner, is to use the standard of the early creeds (Apostle's and Nicene) and the rulings of the first seven ecumenical councils. Using these criteria, which would be the closest approximation to what is believed by "most Christians, in most times, in most places", then the fundamental Protestant doctrines would not be considered heretical, as they do not conflict with the tenets of the creeds, nor the rulings of the councils.

Your point that “Protestants reject almost all the heresies identified by pre-Reformation creeds and councils” is highly significant. There is no difficulty with them using the same words but attaching different meanings because they do not. This is particularly true of the Creed of Nicaea, formulated in 325 A.D. It states,

“We believe in one God, the Father, Almighty, maker of all things visible and invisible;

And in one Lord Jesus Christ, the Son of God, begotten of the Father, only-begotten, that is, from the substance (ousia) of the Father; God from God, Light from Light, Very God from Very God, begotten not made, of one substance (h*m*ousios, consubstantial) with the Father, through whom all things were made, both in heaven and on earth; who for us men and for our salvation came down and was incarnate, was made man, suffered, and rose again on the third day, ascended into heaven, and is coming to judge the living and the dead;

And in the Holy Spirit.

And those who say: ‘There was a time when he was not’, and: ‘Before he was begotten he was not’, and: ‘He came into being from nothing’, or those who pretend that the Son of God is ‘Of another substance (hypostasis), or essence (ousia) [than the Father] or ‘created’ or ‘alterable’ or ‘mutable’, the catholic and apostolic church places under a curse.”

According to that pre-Reformation Creed, Protestants cannot be called heretical. However, that ‘only’ deals with a particular heresy doing the rounds back then. It is one of the most significant, fundamental heresies, it needs to be said, but my point is that Protestants had no quarrel with the meaning of the words of that ancient Creed. They did not attribute different meanings to it, but wholly agreed with the orthodoxly Christian stance stated in that Creed.

We see what the Catholic church would call ‘heresy’ in other areas of belief. And Protestants make no bones about this either – they openly state why they disagree with Catholicism, not attempting subterfuge with cunningly different meanings attached to words. They called a spade a spade back in the day. Perhaps the best example of this lies in the realms of Church authority.

In 1302 Boniface VIII declared in the bull 'Unam Sanctam' that this church has

"one head, Christ and his vicar Peter and the successor of Peter... For all men, it is absolutely necessary for salvation to submit to the Roman Pontiff. This we declare, affirm and proclaim." (DS 872; D 469)

Notice how the one head of the church, Christ, has to share this role with "the successor of Peter" - the Pope? And that there can be no salvation for anyone who does not submit to the Roman Pontiff? That was followed by Pope Clement VI (pope from May 7, 1342, to December 6, 1352):

"No man outside obedience to the Pope of Rome can ultimately be saved. All who have raised themselves against the faith of the Roman Church, and died in final impenitence have been damned, and gone down to Hell." (Source: Pope Clement VI, "Super Quibusdam," as cited in "Apostolic Digest, Book V: The Book of Obedience")

Notice the progression from not obeying the pope to being against the Roman church, to impenitence and damnation?

Protestants protested that their salvation is not connected with bowing down to any man on earth – that you cannot hedge your bets and claim to have faith in Christ alone for salvation, PLUS faith in a Pope! Catholicism claims that whoever does not accept the doctrine of the Roman Church and of the pontiff as the infallible rule of faith from which sacred Scripture derives strength and authority, is a heretic. Protestants put it the other way around. They claim that the infallible rule of faith from which all and any Christian derives strength and authority is sacred Scripture. This means that Protestants cannot bow before any Pope as the 'vicar of Christ' who is supposedly infallible in that role. But Catholics do. This is the main reason why Catholics called Protestants ‘heretics’ back then, and even now: their recognition of Scripture as the supreme source of authority, and not the statements/authority of any pope, also that salvation comes with faith that only what Christ did can save anyone, not with combining such faith with belonging to any organisation or obeying what the head of that organisation requires.