Comment by samus

> The reason why the Tokugawas shut the country's borders for hundreds of years was because they understood that Christian missionaries were a front for a larger invasion force that would pillage the country's resources and abduct people to become slaves in other countries.

They simply didn't want another religion. Buddhism was already troublesome enough with a long history of popular uprisings and many monasteries having become as powerful as daimyos. Oda Nobunaga had been mostly tolerant of religions and also of Christians, but he is infamous for bloody curbing their power. The Tokugawa didn't want any of that from happening again, regardless which religion.

There was also a strong motivation to deflate the power of the port cities. They were often in the hands of untrusted daimyos because the Tokugawa prioritized controlling inland regions with farmland and important road connections to keep the economy running and to ensure that troops could be deployed everywhere and kept supplied in case of rebellions.