One of many reasons may be Constantine's influence on Christianity. In Eusebius' incomplete book Life of Constantine, he recalls a story that [he claims] Constantine told him that while marching his army to battle in 312CE, Constantine had a vision of a cross made of light with the words "In this sign, you will conquer," which was later explained to him during a visitation by Jesus Christ. Constantine then decriminalized Christianity and converted to it himself while also becoming a patron of the Church. Constantine's preferred symbol was the Chi-Rho cross, which largely supplanted the ichthys.

The ichthys (or Jesus fish) was used as something like a secret handshake in early Christianity - because it wasn't an explicit symbol that the layperson could easily associate with Christians (who were being persecuted at the time). Once Constantine converted, though, they didn't have to hide anymore so the ichthys fell out of favor.

The cross symbol as we know it began being used more and more, but the work of Martin Luther may have impacted its modern use significantly. Luther emphasized that the entirety of Christian theology lay in the cross, that only through understanding Christ's suffering can you really know God.