@Beregorn their motivation for killing christians wasnt the same as, say, the attitude christians and muslims had towards each other, though. It was political rather than doctrinal, since christianity was seen as a foreign influence and threat to the shoguns power. A good historical comparison might be the roman empire, which was tolerant of most religions but persecuted christianity because it undermined the state. Both were extremely authoritarian but part of their strategy to maintain power was a syncretic attitude towards religion
EDIT: 2 seconds after i submitted this comment i realized how insanely out of place it is in the comments for this comic in particular