Elizabeth Tudor could have been executed during Mary reign simple because she did not want to change her faith and become a catholic.
Her reluctance to convert to Catholicism made Mary wary of Elizabeth and dislike having her as her heir, but really Mary was also vigilant of her because of Elizabeth’s connections to treason in 1554. Elizabeth was imprisoned and interrogated in the Tower because of the evidence suggesting her involvement with Thomas Wyatt a figure head in the rebellion of 1554 and not because she was a Protestant of sorts.
But overall this was period where Catholic and Protestant monarchs did persecute their religious opponents for theological and political reasons.
‘Noli me tangere; for Caesar's I am’
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