From the article. I read this as Chick-fil-A has simply changed the method by which donations to those 3 organizations will be given.
“The new giving structure moves away from the multiyear commitments Chick-fil-A had with the Salvation Army and the FCA and focuses on annual grants, which Tassopoulos said will be reviewed and assessed each year. Future partners could include faith-based and non-faith-based charities, but the company said none of the organizations have anti-LGBT positions.”
There you go with facts!