You think it's not historical for the religions featured in this game to have Inquisitor units or act aggressively toward each other? Keep in mind it doesn't matter what the actual adherents of said religions supposedly populating these religions in-game think, this is all about the policies a shrewd leader is adopting out of expediency. You can read an insult into that if you want but the way this game presents it religion is entirely mechanistic and manipulative, not unlike "Declarations of Friendship" and various other overtures of good will that are in fact strategic and political.
PS might be informing to look up a certain number of Popes with the name "Pius."
The Piety tree is about using religion... eliminating other religions is ONE way to use it... Having benefits to other religions is another way.
Essentially stealing some of their benefits (taking some of someone's UA).. sounds machiavellean enough for me.. like "Universal Suffreage" to keep the petty bourgeoius rabble quiet.
The problem is the Game mechanic of spread religion does not currently support secondary religions... (ie only majority religions that control a city can spread from that city)... on the other hand if a Piety Policy both made it Possible and Beneficial to have secondary religions it would be good.
I would say religious tolerance should
1. give you a benefit to having other religions in your cities (already does that)
2. give you a way to maintain them as Secondary religions (+2 pressure on Standard for city founder's religion, Pantheon and for Any world religions with 1+ followers in Your civ.. not this city, your civ) x 3(+6 instead of +2) for Your religion/pantheon
(your cities would get +6 of your religion/pantheon..+2 for other religions.. your Captured cities would get +2 of the native pantheon.. +2 of other religions, and +6 of your religion if you had a full religion)
This would allow you to run a religiously tolerant pantheon only "Roman empire"... each city keeps the pantheon of its founding civ.. and receives the benefits thereof
This would also make it a lot easier to maintain your religion in cities against enemy missionaries... and you would have a secondary religion available all of your cities...
And if it is ALL Pantheon beliefs available give a benefit, all of those religions would be useful (especially including ressurecting foreign pantheons.. or preserving your own, which would be fun).
[get a Pantheon, but miss out on religion... go Religious Tolerance and get your Pantheon back.. in every city you founded]