If marriage equality was popular it would be legal everywhere
Marriage equality will be popular in the not too disant future (5-10-15 years?) but it is not popular yet. Heck, president Obama was against marriage equality only a few months ago. Something like 35 states explicitly outlaw it.
It is legal in only a few places, and those unions are not recognized elsewhere. (Which is unconstitutional, IMO, but so is a lot of stuff)
Polling has moved a lot over the years. Marriage equality is much more popular than before -- it is roughly as popular as legalizing marijuana. Marriage equality has only a slight edge over pot... marriage equality is favored, nationally, about 48%-44%.
Think of marriage equality like marijuana and it is not at all surprising that some CEO would feel perfectly comfortable speaking against it.
The demographics mean that as the younger generation takes over marriage equality will someday be the law of the land.
But we are not there yet. Marriage equality is not the general American position. 48%-44% is not a consensus.
So of course some bigots will show the flag at Chick-fil-a. No need to find that discouraging. It is a contentious and roughly 50-50 issue.
The "out" bigots will die off over time, but marriage equality is not net popular. Yet.