Being Catholic was also seen as treason. The rest I’m sure you do know about, my history is crap but even I know that Catholics had a bit of rough time during the reform.
Both Catholics and Protestants had a rough time during the reformation, depending on which monarch was in charge. But even then, the government didn’t go around burning thousands of people just for being catholic or Protestant.
Buy the time of the Gunpowder plot the reformation was long over and England was firmly Protestant. Catholics were persecuted and occasionally executed (mainly the priests) but in the main the persecution was at the level of debarring them from certain offices etc. And this persecution was more due to the failure to observe the beliefs of the Church of England rather than being catholic per se.
It was the removal of this persecution that in part cause the Glorious revolution in 1688.
The thing about the 17th century was that for most of the time people were shit scared of the Pope and his Jesuits minions over throwing the British Monarchy and imposing the Catholic religion. (Think like the Dail Mail and the Muslim menace hiding behind the Burkha, only worse). The Gunpowder plot was just one of these supposed Popish attempts to overthrow the monarchy.
So when Catholics were executed, it was because of a perceived link with this effort to overthrow the monarchy and hence treason, rather than being Catholic. (but it really does get difficult to separate religion from politics).
Most Stuart Monarchs were rather partial to Catholic beliefs anyway. – Divine right of Kings and all that.
Anyway, academics have written vast tomes on this and nobody has yet come up with a definite answer, so I may be wrong.