Ter:
Nobody denies that terrible things were done within the Church in the past (partly because judicial punishment was much harsher in all walks of life). However in the most part those acts were political opportunism rather than ‘religious’.
For example: it is estimated that about 3/4 of the catholic population of Ireland were killed during the Cromwellian Plantations (in the 1600s) & most of the rest were forced to move West to Connacht and we had the Penal Laws (priests killed, massgoers killed, catholic couldn’t vote or own land etc.) Offically this was because we were ‘Popish’. In reality if was because a) English Lords wanted the land & b) Britain was afraid that Spain/France would use Ireland as a launching pad to attack England.
I wonder what the real figures are - after seeing very inflated figures for Catholics killed under Elizabeth, one learns to be healthily sceptical 
No Protestants could vote in England, who did not satisfy certain socio-economic tests; so denying the vote to Catholics would hardly count as particularly unfair. No Protestant women could vote at that time. Women had no vote in general elections until 1918.
And in 1571 or so, there had been a “Popish plot” - the Ridolfi Plot. In 1569, there was the Northern Rising; the Bull of Pius V attempting to depose Elizabeth in 1570; the Babington Plot against Queen Elizabeth in 1586; the Spanish Armada in 1588; and a stream of pamphlets by certain disloyal Jesuits such as Father Robert Persons, calling for Elizabeth to be dethroned, and for Philip II to replace her - which would have made Spain even mightier than it was already.
As well as Catholic plotting in Scotland: James VI & I had good reasons to fear treason, and to strengthen the English Protestant Church; his experience and that of Elizabeth I affected their policies, inevitably. And at this time, policy depended as much on the monarch as on the Parliaments. After 1688, Parliament became more important than the monarch.
So it is unsurprising that Catholics came to be regarded as traitors - some were, and deserved all they got. Especially since kingship was sacred, and so were monarchs.
The policies of Elizabeth and James VI & I are entirely intelligible, given their own experiences and the history of the English & Scottish Reformations.
As well as persecution of Protestants on the continent. Catholic and Protestant rulers alike used espionage and murder as instruments of politics, both were ready to stir up rebellion in the lands ruled by their enemies; and the resulting insecurity in England (and Scotland) has to be taken into account; Britain, in both parts, was a Protestant island amid a host of potential enemies, so it had to play them off against each other, and control its own potentially disloyal population.
This goes a long way to explain English atrocities in Ireland, and attempts to subdue the O’Neills and Fitzgeralds, for example; Ireland was very hard tto control, and was well-placed to be a backdoor to the British mainland.
Besides, almost no state at that time had much room for populations which differed in religion from the majority - religion and politics were almost everywhere identified. Which is why loyalty to the Elizabethan Settlement was so important in England; and why Louis XIV in 1685 persecuted the Protestants into becoming Catholics; an absolutist monarchy such as France had to be sure of the loyalty of its subjects; so they had to be Catholics. ##
