Rev Cardy admitted he isn't sure whether the thieves stole it because they liked it or because they hated it.
"Some people don't like the billboard because they like Donald Trump.
"Some don't like the billboard because it infers Jesus was a loser.
"Whereas others, like myself and those here at the community of St Luke, see the cartoon as showing that the values and views of people like Mr Trump are completely at odds with those of Jesus.
"It is disappointing that someone decided to break the law and steal something that was stimulating a meaningful discussion in our community about the meaning of Easter."
St Luke's will be replacing the billboard after the church's Easter Sunday celebrations of the resurrection of Jesus, and intends to keep the billboard up as long as the issue of Trump's candidacy remains undecided.
In a statement about the billboard released on the day it was erected, Rev Cardy said: "For those of us at St Luke's, the cross is about politics.
"Jesus was killed, violently, publicly and shamefully, because he spoke truth to power and confronted the leaders of his day about their treatment of the outcasts.
"To the Trumps of his day, and to those who see winders as having money and power, the Jesus of the Bible, was a loser who associated with those rejected by society."