Philemon hosted the church meetings in his home. He was willing to put up with people bringing in mud onto his cream carpets.
Who says he did not ask those attending to politely remove their shoes? I certainly would have done.
It is generally thought that ancient Greeks removed their shoes when entering homes. I am not certain of Philemon's ethnicity, but he was probably more likely to have been Greek than Roman (the Romans kept their shoes on in homes).