A lot of historians (I've noticed) seem to deduce that there is generally negative intent behind writing and I don't really understand why.
Einhard wrote about Charlemagne the Great in the early to mid 800s AD (The Life of Charlemagne) and is a perfect example because I have heard his book labeled as a propaganda piece. That suggests that Einhard's intentions of endorsing Charlemagne were to indoctrinate their people. But what would the point of that be since the Franks were already... Franks? Besides their assumed loyalty, there is evidence to suggest that the Franks had reason to support Charlemagne. So why would their affection towards him have devious intent?
I can see the connection between Charlemagne and Augustus Caesar; and perhaps this is implying in his (and by extension the Franks) cultural superiority.... and yet Charlemagne's kingdom was already prosperous without the Romans. Where I can see the benefit in a country that is relatively small and unknown aligning itself with Rome, the Franks had their own thing going for them and already had a good relationship with the pope.
Maybe Einhard wrote this for the Roman populace when Charlemagne became the Roman emperor attempting to ease the transition of two cultures coming together. But I don't feel like that should be considered propaganda-- saying, "Hey, don't worry Charlemagne is great", seems rather welcoming.
Regardless of this piece, I seem to hear a lot from multiple sources that people writing in history at the time are purposefully deceiving the reader. But how do we know that? Even if there are conflicting stories, why assume that someone is lying (in that lying is intentional). Sure, some writing is clearly propaganda... but not everything is meant to self-serve, right?
Geoffrey of Monmouth also gets a lot of hate for his History of the Kings of Britain.
I think my first response to your question would be in a more general sense. In many ways historians, especially of the early middle ages, are reacting to an older trend to read the sources more or less at face value without in many instances a deeper questioning of the circumstances surrounding their production.
Now, Einhard's Vita Caroli is a good example! Some points need to be made however, even if we are to label Einhard's work propaganda, it does not necessarily mean he was attempting to “indoctrinate” the people. Einhard's work, while popular, was confined more or less to the highest echelons of society. While there certainly are texts that were produced that were meant to foster some sort of ethnic identity, I would argue that the Vita Caroli is not one of them. Also, I would caution against a sort of equality between propaganda and a malicious intent, historians of the ancient and medieval worlds would not have particularly seen it that way and even today I don't know if we can make such a strict division.
So then why did Einhard write his work? The answer in part depends on when you date it. I personally believe Rosamond McKitterick's argument that it should be dated early in Louis the Pious' reign (814-840).^1 Her argument is that Einhard wrote his work in part in order to glorify Charlemagne (whom Einhard was rather close to) and that it was meant to smooth over the succession of Louis the Pious in 814. McKitterick believes it was written in connection with Louis' own plan for succession, the Ordinatio Imperii in 817, and that it was in part designed to stress the legitimacy and strength of the dynasty. Just because Einhard has a purpose does not mean he is deceiving anyone, indeed the audiences reading Einhard would have been alive during Charlemagne's life for the most part, and may have known him. However Einhard can distort or interpret these common narratives in order to make a point.
On the coronation, again Einhard is distorting his narrative slightly. The debate about whether Charlemagne actually knew he was to be crowned emperor in 800 has largely come down in favor of him having knowledge, but Einhard's statement is now usually interpreted in the sense of older imperial tropes about humility.
That is sort of a broad overview of some of the things you raise in your question. Although most historians nowadays I can't imagine assuming that people writing history were purposefully deceiving the reader, that seems much too strong. What have you been reading in particular? In regards to early medieval stuff I could maybe shed some further light on why they are interpreting it that way!