In order to appease their sponsors, Real Madrid decided to alter their logo by removing the cross on the cress. The cross used to appear just above the logo.
Real Madrid first unveiled a cress with a cross on top of a crown in 1920, and have displayed a similar crest uninterrupted since 1941. The crest doesn’t have a cross because the club has any particular religious affiliation, but simply because that’s what the royal monogram of King Alfonso XIII (and many others) looked like.
But this is not 1920, and Real Madrid’s reach has expanded far beyond Spain. They’re signing extremely lucrative sponsorship deals in the Middle East, and one such deal in Abu Dhabi has caused them to adopt an alternative version of the crest without the cross. It should be noted that Madrid haven’t changed their crest, they just use a different one in countries where it doesn’t make business sense to have an affiliation with Christianity, or display any Christian imagery as part of their crest at all.