His bail was set at $7 million.
Castillo serves at Our Lady of Guadalupe Church and is known as "Father Alex."
Police said Castillo met his alleged victim through the church, where he's been a fixture for seven years.
"My kids love him so much and everybody in my family is so sad about what is happening with him," said parishioner Sucely Estrada of Ontario.
Estrada said she doesn't believe the charges.
"He's the most wonderful person I have ever met, and I really love him a lot," Estrada said. "I'm so sad about it."
As shocking as the allegations are to parishioners at the church, detectives think there may be other victims and are asking suspicious parents to contact them with information.
Castillo could face up to 22 years in prison on the charges.
"This kind of activity doesn't happen just once," said Sgt. Dave McBride of the Ontario Police Department. "We see multiple victims."
Ontario police are already reviewing claims from another boy, who is 14-years old.
Investigators have decided not to file charges on behalf of a third child because the statute of limitations has expired.
Two other alleged victims were apparently over the age of 18.
Meantime, the Diocese of San Bernardino is offering support for the alleged victims.
"We take the opportunity again today in light of this to express our deep sorrow and regret for all the victims of abuse, both in the church and society at large," said John Andrew of the Diocese of San Bernardino. "It's a terrible problem."
Castillo has pleaded not guilty.