To be honest, I've only ever read "The Merchant of Venice" once. Shylock has been variously studied as both a sympathetic character and as a negative one. When the play was written, Jews had not lived in England since the year 1290, and were not permitted to do so again until 1656 under Oliver Cromwell.
Englishmen generally knew nothing about Jews, and the only thing that they thought about them was a vague negative concept of them as moneylenders. Was England Judeophobic during Shakespeare's time? Probably. Did it matter? Most likely not. To put it bluntly, I doubt the average Englishman who watched the play gave much more than two shits about that aspect, except to say, oh, what a filthy Jew. If asked, I expect his response would have been something along the lines of "Ugh, a Jew. Go away."
No, I have no beef with Shakespeare over his portrayal of Shylock. He was merely reflecting the broader English perspective, and for that matter, the broader European view. Except that Europeans continentally were often MUCH more ferociously anti-Semitic than Englishmen ever thought of being!
I think Shakespeare was interested in history, but only insofar as it served the greater purpose (in his mind) of helping to penetrate the deeper puzzle that lay behind "people's motives, thoughts, and interactions", as you so well put it. I actually think he was a decent historian, so long as that greater purpose was not lost, AND so long as he did not piss off the wrong people and lose his livelyhood or his head.
The biggest problem I think that both England and America have is that we see English history in large part THROUGH the lens of Shakespeare, whether we care to admit it or not. I mean, even now, when we have found the bones of Richard III, how many newspapers have had to say that he was NOT hunchbacked? In fact, it DOES appear that one shoulder was slightly lower than the other, but not enough to mess him up per se.
So, how much more do we see through Shakespeare? I mean, I am not saying the Master's Degrees, the Doctors. I am saying the average college graduate or high school graduate. And God forbid the people that don't have an education!
Granted, England's educational system is better than ours, that can't be denied, so they might do a bit better, but still.The Tudors, and Shakespeare, did a damn fine job, of shaping history to their will.
MAJOR EDIT:
It should be noted that there are some scholars who believe that the Tudors (particularly Henry VIII) tolerated secret Jews at the court, possibly even allowing a secret synagogue to function. Although there is no conclusive proof of this, there are some rather suspicious names that appear to be Jewish, both Spanish and especially Italian, musicians, who wrote music for the court. Many of them were, of course, members of the Church, presumably converts (first Roman Church, and later English Church), but it appears that some may have been secret Jews that Henry may have known about and tolerated. In fact, some appear to have written music for Jewish prayers. I actually have a CD of Jewish musicians at the Tudor court that includes a few Jewish prayers on it. So, there you are, for whatever its worth.