Cromwell granted religious toleration to all Protestants and Jews. Quakers and Catholics had the right to worship privately, but could not proselytize.
Catholics were denied the right to move more than 5 miles outside their home without special permission, even if they were sick, visiting the market etc. Cromwell was military astute, but when it came to government he was pretty poor, dismissing the Rump because of fears they might have elections that would return an anti-Commonwealth, or Cromwellian majority. Neither could he rule with the army, so he decided to self impose a protectorate and dictatorship.
His followers also had no right to execute a foreign king. Okay, self preserving Scottish nobles and soldiers handed him over but 'axing' the second Scottish monarch in 100 years was a bit much....
Lean villain