Why does Onesimus cause a problem for paedobaptists? Well a lot has been made in their argument of the descriptions of converts being baptised with their whole households. The argument is that it would run contrary to the culture for people to be only baptized if they repented themselves. Rather, we would expect them to take the faith of the head of the household.
However, when Paul writes to Philemon about his previously useless slave, Onesimus, he describes him as someone who has now moved from being that to being like a son to him and a brother to Philemon.
If Onesimus had been included in the church through baptism, at that point, his status and relationship to other Christians would have changed. However, it is clear that the status came not through Philemon’s faith but Onesimus’ own conversion and faith.
Now, I appreciate that some will come back and say that Onesimus was only part of the visible church through the household baptism. However, this is to misunderstand what is meant by the visible and invisible church.
The invisible church is the people of God throughout history so includes all who have died and are now with Christ. The visible church refers to the church that is visible in the world today. This does mean it will include people who are not true believers but that is due to the fallibility of human discernment. It does not mean that we don’t treat those in the visible church as less than believers. So Onesimus should always have been treated as a brother.
The Onesimus case simply does not fit with a paedobaptistic/household baptism/faith model.