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'I am the one who gave Nagato the Rinnegan.' That's probably why people think it was Tobi.
This manga isn't about everyone in the entire world. It's about the Senju and the Uchiha, the people of the ninja world. Everyone in the Manga is either a direct descendent of the Senju, or a direct descendent of the Uchiha.
Fact.
And I'll say this again:
UNTIL KISHI EXPLAINS IT WE ONLY HAVE WHAT THE MANGA TELLS US TO GO BY. THE MANGA TELLS US THAT TOBI GAVE NAGATO THE RINNEGAN. THEREFORE, TOBI GAVE NAGATO THE RINNEGAN.
Because the Rinnegan is an ocular jutsu, the final form of the Sharingan. Only Uchiha can possess it naturally without some sort of an eye implant. So either Nagato is an Uchiha, or it was given to him by an Uchiha.
Not sure why that's so hard for people to understand, especially when it's been revealed in the Manga that Nagato is an Uzumaki (direct descendant of the Senju) and that Tobi gave him the Rinnegan.