When translated into English the sea goddess thing can be really weird, but Ma Zhu is not really a sea goddess. She's more like a folk symbol combined with a patron/saint of the sea and a semi-lifestyle religion. With Taiwan being an island, the patron saint of the sea is an immensely important part of the culture.
She is widely known and revered in all of Taiwan. When you go to a Taiwanese family and say "Mazhu bao yo" (Mazu bless you) - it's generally well received even if the people don't believe in Taoism or natural / personified deities.
The idea that Gou says "Mazu wanted me to do it" is more like saying to a Catholic that Mother Teresa inspired you to visit India and start a non-profit agency to help the people there.
Hopefully the analogy holds for people who are not familiar with the culture there.