What's rather amazing with their affair is that it was kept secret for so long.
I find it impossible to believe, with the number of security people around both of them, that Charles didn't know. Their ultimate loyalty is to Her Majesty, not her son, and certainly not to her son's wife. I am quite certain that the Queen knew about the escapades from the get-go, and so did Charles.
As someone brought up in that world, I would imagine that Charles saw it as how things are; however he may have felt about Diana personally, he married her out of duty. His job was to provide continuity, an heir to the throne. That he picked a young, beautiful, incredibly photogenic, endearing bride is simply not an accident by any stretch of the imagination. He may well have loved her. Seeing early photos and footage of them would seem to indicate that if he didn't love
qua love her, he certainly felt a very strong fondness for her, which was a happy accident.
In the real world, royal marriages have historically been nothing about love. They have been about duty and alliance and
not one thing more. That love arose from some of them is secondary to the main issue. Therefore, once the heir (and spare) had been begotten, most couples in such marriages took it as tacitly understood that they would undertake their own sexual and emotional affairs outside the marriage in order to fulfill the desire that most of us have to be wanted and to be loved. To put it another way: royal marriages, historically, are about contracts. They take lovers to deal with the emotional side of their lives.
That either Charles or Diana had affairs is singularly unremarkable. I would suggest that you look at the history of royal and noble marriages if you disagree. That they both so publicly admitted them is what is astonishing.
Moving back to the point... The Queen has been described--by one of her own sons, nonetheless--as having the best spy network within the Palace. He, and many staff, have commented that she knows everything. That she wouldn't have known about the Hewitt affair--or, indeed, the Camilla affair--simply beggars belief. It is possible that she wouldn't have told Charles, but extremely unlikely; after all, he has been groomed for the throne for almost 60 years now, which would obviously include understandings of how the world
really is versus how he would wish it to be.
The affair may have been kept secret from the public, but it is fundamentally impossible that it was kept secret from the Queen, her son, or the Grey Men of Westminster.