First, the excesses of the Inquisition in Spain where condemned by the Pope at the time.
The Inquisition only had juridiction over Catholics, some of those Catholics had forefathers that where originally Jewish, some of the people brought before the Inquisition where charged with Adultery, others charged with practicing Lutheranism in secret, or reverting to Judiasm in secret.
Unlike the modern day where the Church and State are separate, all over Europe the Religion of the State was the religion of the Prince or King. Anyone who practiced other religions was suspect of conspirasy against the State. So in Holland, England, Switzerland and parts of Germany, after the Reformation, Catholics who practiced their religion in secret where arrested by the State and either jailed and fined, or killed. In Spain the Government would arrest and turn over to the Church people suspected of religious crimes. One very interesting aspect of the Spanish Inquisition, was that people arrested of non-religious infractions tried to get their cases transferred from the Civil Courts to the Inquisitions courts, because unlike the Protestant courts in other countries, the Inquisition was much more lenient and believed in repentance. Many Protestant courts believed that if you practiced a religion other than the State religion you where unsaved, and did not allow repentance. Most of the people convicted by the Inquisition where either fined or given a punishment like wearing a symbol of their crime on their clothing for a period of time, and then returned to “normal” life. In Calvin and Queen Elizabeth’s courts one was usually treated much more harshly.