He was noted for his devout Roman Catholic beliefs and his strong support for the Irish Catholic political cause; this led him during the Irish Rebellion of 1641 and the ensuing Civil Wars to play a double game, offering support to both the Crown and the rebels, with the result that no party to the conflict fully trusted him.
In November 1632, shortly after the appointment of Thomas Wentworth, 1st Earl of Strafford as Lord Deputy of Ireland, John and other prominent Catholics petitioned him not to enforce the Penal Laws.
The Crown's legal advice was that a clear case for treason had been made out against John, but that no Meath jury would convict him, so that if possible he should be tried in Dublin.
[7] Under the Act for the Settlement of Ireland 1652 John and his father were both exempted from pardon for their lives and estates, but do not seem to have suffered any actual ill-treatment.
John moved to England where his wife Elizabeth Weston argued successfully that as an English subject she was entitled to enjoy part of the Netterville property.