This was a request for information and an inquiry from Nuh concerning the cirumstances of his son's drowning.
(and said, "O my Lord! Verily, my son is of my family!") This means, "Verily, You promised to save my family and Your promise is the truth that does not fail. Therefore, how can he (my son) be drowned and You are the Most Just of the judges"
(He (Allah) said: "O Nuh! Surely, he is not of your family...") This means, "He (your son) is not of those whom I promised to save. I only promised you that I would save those of your family who believe." For this reason Allah said,
l(and your family except him against whom the Word has already gone forth.) 11:40 Thus, for his son, it had already been decreed that he would be drowned due to his disbelief and his opposition to his father, the Prophet of Allah, Nuh peace be upon him. Concerning Allah's statement,
(Surely, he is not of your family;) meaning that he (Nuh's son) was not among those whom Allah promised to save. `Abdur-Razzaq recorded that Ibn `Abbas said, "He was the son of Nuh, but he opposed him in deeds and intention." `Ikrimah said in some of the modes of recitation it said here, (إِنَّهُ عَمِلَ عَمَلًا غَيْرَ صَالِحٍ) "Verily, he (Nuh's son) worked deeds that were not righteous."