Holy *add an explitive here* VH is very hard.

[Martok]

I never attacked first so they all should have been excommunicated?!

True. But as you probably already know, a Catholic faction that attacks another Catholic faction will only be excommed if it has twice as many provinces as its opponent. Since you're (initially) much bigger than your neighbors, that's why they can get away with attacking you while avoiding receiving a Papal edict against further incursions. No it's not entirely fair, but that's the game for ya.