Why do you say Taiwan has zero Christian background? Do you know why Korea receives preferential treatment? (or have you ever wondered why and how)
Anyways It's the ideas and the spirits that matter.
Not only that, the centred cross can represent justice and balance. It can represent the goal of democratic process, of achieving a consensus. The straight lines represent rule of law. The Cartesian x-y-z represents Taiwan's inherent role and responsibility as the fulcrum and stabilizer of the Pacific. A cross is a cross and needs not take on a Christian interpretation only.
The two orthogonal lines point beyond the horizon in 4 directions, representing our visions and ambitions beyond the confine of the island.
The green colour reminds the people forever the geography, that this is an evergreen island and that the Formosan people owes its life and everything to this island's fertility. Sole allegiance to this island ONLY, and not to a for-profit, nomadic banner-organization and not a fake animal such as the dragon.
Orthogonal lines crossing each other also represents independence, and even represents that each individual is independent and individual right is also of paramount.
If you rotate it in whatever way (whatever perspective), the integrity of the Evergreen Formosa Flag is not distorted or diminished. This represents STRENGTH.