Before the Spaniards came here.. the ethnic people of Cebu, Bohol and Butuan have already established their own settlements and kingdom, that's why we share a common language and culture amongst each other.
Meanwhile, the other ethnic peoples such as the Tagalog had their own kingdom as well, hence the difference in language and culture.
The only reason why we became "one country" and eventually "Filipinos" was because the Spanish conquistadors thought it would be a good idea to claim all the surrounding islands for the Kingdom of Spain and merge them as one. That's just it.
I study history and linguistics, but if you'd like to know more, just message me and I can recommend some books you can refer to if you guys are interested.
But at the end of the day, I would like to say that even though if we have a different past, different language and different culture, it would be best if we all gathered together as one instead of fighting one another. We should all be friends and aim for the betterment of this country. Change does not start from your government or ethnicity, but from yourself.