I am not a Czech but I know some answers. Some information about jews in Bohemia can be explained with father of king Wenceslaus IV who is important character in the game. His father was Charles IV, and like Wenceslaus also Charles has often problems with money. So he let jews pay for their security to gain a new source of income.
As the black death starts, a french jew confess in torture he had poisoned some wells and start the black death. This news spread about all over europe and jews in all countries get murdered and blamed about black death. This was not good, not only for the jews, also for the emperor who need them to pay taxes.
People don´t liked the jews and wanted to kill them. So Charles get the jews under his security. But he had not enough might to do it in the whole HRE, it was a system of feudalism. Emeror in HRE never had absolute power. So he sell some of the jews to cities and rulers who killed or banned them. They also had another notion in mind. Jews often deal with money, and many people get debts at the jews. So if they kill the jews, they also could burn their debenture. No debts anymore if the jews die.
The black death was not a problem in Bohemia and especially in Prague and Charles IV had all his power in this country, because it was his property. So while he sells his jews in most areas of HRE, he was able to guard them in bohemia. They were important, because jews pay for this kind of security.
Its not about more friedly people in Bohemia, but with no black death at their place they don´t need to blame the jews, and the ruler of Bohemia was the Emperor himself, and he needed his jews. Unlike as in other parts of HRE here he had the power to protect them.
I don´t know exactly how it was in 1403, but worst phase of black death was over, and I can imagine also son of Charles, Wenceslaus used the jews to get more taxes.