Speaking on RTÉ Radio's News at One, Mr Goan said he could categorically assure license fee payers that they would not lose out as a result of the deal.
He said he regrets remarks made in the Dáil today and that RTÉ's independence is central to any decision he makes.
Mr Goan said the issue was one of debt collection and that he believes what RTÉ got in a debt collection situation was best possible deal and had the station pursued the matter further it may have got less money.
Earlier in the Dáil, Taoiseach Bertie Ahern categorically denied that he intervened in the settlement.
However, Labour leader Pat Rabbitte said 'if you believed in the tooth fairy' you might think there was a coincidence between RTÉ reaching a settlement with Deputy Flynn a couple of days after the Taoiseach said her future lay within Fianna Fáil.
The Taoiseach today faced questions from Opposition leaders about agreements he had reached with the four Independent TDs who are supporting his Government.
Fine Gael leader Enda Kenny claimed licence fee payers were outraged at Ms Flynn's settlement with RTÉ, and asked whether there was a deal between her and the Taoiseach.
Mr Ahern said he had not discussed the case with her, and that RTÉ's independence was 'well known'.
He described suggestions that he was involved as 'sinister', and said they were 100% untrue.
But Mr Rabbitte said no one was suggesting there had been direct pressure.
