I have read the decision in its entirety and understand that, thanks.
Good couple of (actually more than a couple...4) paragraphs from oyez.com explaining why they decided the way they did in this particular case despite that.
“The Court explained that while gay persons and same-sex couples are afforded civil rights protections under the laws and the Constitution, religious and philosophical objections to same-sex marriage are protected views and can also be protected forms of expression. The Colorado law at issue in this case, which prohibited discrimination against gay people in purchasing products and services, had to be applied in a neutral manner with regard to religion. The majority stated that Phillips' claim that creating cakes was a form of artistic expression was required to be afforded Free Speech protections, and were a component of his sincere religious beliefs.
The Court also explained that in 2012, the year that Phillips refused his services to Craig and Mullins, the law in Colorado and across the country with regard to same sex marriage was much more unsettled than it became after United States v. Windsor, 570 US 744 (2013) and Obergefell v. Hodges, 576 US ___ (2015). At the time, the State Civil Rights Division had also concluded in at least three other cases that bakers had acted lawfully in declining to serve same sex couples. Thus it was not unreasonable for Phillips to believe that he was acting lawfully at the time, and his claims before the Commission were entitled to neutral treatment.
However, the Court stated that Phillips did not receive this neutral treatment, with members of the Commission showing clear and impermissible hostility toward his religious beliefs. The Court explained that commissioners' comments disparaging Phillips' beliefs and characterizing them as rhetorical were inappropriate, though these comments were not mentioned or disavowed in subsequent legal proceedings. The Court concluded that these comments cast doubt on the fairness of the Commission's consideration of Phillips' claims. The Court also pointed out that disparities between Phillips' case and those of other bakers with objections to making cakes with anti-gay messages, and who were victorious before the Commission, further reflected hostility toward the religious basis for Phillips' position.
The Court concluded that the Commission's actions violated the State's duty under the First Amendment not to use hostility toward religion or a religious viewpoint as a basis for laws or regulations. Under the facts of this case, the Court determined that Phillips' religious justification for his refusal to serve Craig and Mullins was not afforded the neutral treatment mandated by the Free Exercise Clause.”