Paul’s question isn't just about if they were baptized, but into what. What does baptism truly signify?
When Paul asks, 'Into what then were you baptized?', he's getting to the heart of their spiritual identity. Baptism, in the New Testament, signifies a deep identification with the message and the person who is doing the baptizing.
It's like saying, 'I pledge my allegiance to this teaching, this way of life, and to the one who represents it.' For John's disciples, this meant a commitment to John's message of repentance and his proclamation of the coming Messiah.
However, as the commentary notes, John's baptism looked forward to Jesus. His disciples understood Jesus as the Christ, but they hadn't yet received the fullness of what Jesus's death and resurrection, and the coming of the Holy Spirit, would mean. Their baptism was into John's prophetic message, but not yet into the completed work of Christ.