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.
I am glad I don’t work for you. If a private company can fire someone for voicing their religious belief but allows a gay person to voice and show their sexual belief, isn’t that discriminatory? Did this guy demand the LGBT symbols be taken down? No. He answered a question that was asked apparently. So he can’t be truthful to himself?