Threat
When some Japanese people converted and combined their faith with a demand for political control, the Shogunate reacted with uncompromising force. The Shogunate viewed Japanese Christians as the advance guard of the Colonial Powers. The Shogunate felt that its unilateral control of a unified Japanese state was threatened.
Initially, Portuguese had entered Japan as trade negotiators, but many Jesuits had been sent on missionary work by Portugal in coordination with the Vatican. The first Jesuit to enter Japan was St. Francis Xavier in 1549 on a Portuguese ship.
In 1615, bands of Christian samurai fought against Shogun Tokugawa Iemitsu and lost. In 1618, the Shogunate enforced a full-scale prosecution of native Christians and missionaries.
Rebellion Put Down
The precipitating cause of the more draconian sakoku policy was the 1637 Shimabara Rebellion where thirty thousand peasants, who had openly proclaimed their allegiance to Christianity, tried to maintain a stronghold on the Shimabara Peninsula east of Nagasaki.
With the help of a Dutch naval bombardment, the peasants were massacred. Eighteen months after the rebellion began, a stricter sakoku policy was implemented, Japanese Christians were actively hunted and forced to recant their faith in public by stepping on a votive image. If not, they were tortured and killed.
The authorities wanted to split private thought from political action. It looked like stepping on a votive image forced Japanese Christians to expose their private thought to make it null politically.
You find it outrageous that a government forced members of a faith to recant so publicly. It is a sort of reverse communion.