Under Focus Points from Multiple Sources the book reads:
It’s possible, especially through archetypes, to gain focus spells and Focus Points from more than one source. If this happens, you have just one focus pool, adding all the Focus Points together to determine the total size of your pool. (Remember that the maximum number of Focus Points a pool can have is 3.) If you have multiple abilities that give you a focus pool, each one adds 1 Focus Point to your pool. (Core Rulebook pg. 302)
It's not clear to me if taking the same feat multiple times counts as more than one source, or multiple abilities, for the sake of getting an additional focus point. Specifically, the Domain Initiate cleric feat doesn't seem to mention anything on the issue.
The Domain Initiate cleric feat reads:
Special You can select this feat multiple times, selecting a different domain each time and gaining its domain spell. (Core Rulebook pg. 121)