Because the main issue was constitutional, not whether the king was alive or dead. The issue with Charles I, his father, and James II was (ultimately) that they did stuff that really pissed everyone off (and were often very disinterested leaders)...which was to a large extent based on a difference of opinion about what being king actually meant (even in today's authoritarian regimes, there is a concept of ruling with the consent of the people...China is a good example of this).
The religious motivation is fairly simple if you consider the period slightly before: Spain was predominant, England had gone to war with Spain, England was relatively weak, and Catholics had just tried to blow up Parliament...yes, England had lots of Catholics near government (which ended up being part of the problem) but it was a Protestant nation (the Thirty Years War happened in Europe too, this kind of religious conflict was not unknown). The extreme position that Cromwell took was also probably not a reflection of public opinion either btw (he was unquestionably not the leader of some democratic cause, and he just stepped into a power vacuum with leadership that was lacking elsewhere...the majority of his notable actions would be called religious genocide today).
To see the religious issue more clearly btw: if England had indeed had a Catholic ruler, it would have been like the Spanish Netherlands...that is the fear that existed at the time.