This is a private company. They can fly whatever flag they want. They are not stopping people from practicing their religion. If I don’t like the company displaying the flag, I can choose to not work there or I can work there and ignore it. This is not a freedom of religion issue; employees can practice whatever religion they choose.
The NFL is a private company. They can require employees to not wear political symbols on their uniforms; they can require employees to stand at attention when the national anthem is played. This is not a freedom of speech issue; employees can speak freely on their own time.