Going purely from Census entries Joseph was the Son of Charles/Rebecca.
Birth Reg GRO;
BUTLER, JOSEPH, Mothers mn HUGHES ***
GRO Reference: 1847 M Quarter in KINGSCLERE Volume 07 Page 110
Marriage of his Parents is on FreeREG 30 Oct 1841 with their Fathers names/occp's
His Fathers Bapt 1816 Kingsclere
Although Rebecca names a Father on the M/C I think she was illeg.
REBEKAH Hughes christened 22 July 1821 Caversham, Oxfordshire, Mother ANN Hughes
(Familysearch.Org)