This was answered by Allah Himself when Abraham (AS) asked Him about His progeny:
وَإِذِ ابْتَلَى إِبْرَاهِيمَ رَبُّهُ بِكَلِمَاتٍ فَأَتَمَّهُنَّ قَالَ إِنِّي جَاعِلُكَ لِلنَّاسِ إِمَامًا قَالَ وَمِن ذُرِّيَّتِي قَالَ لاَ يَنَالُ عَهْدِي الظَّالِمِينَ
And recall when Abraham was put to trial by His Lord in a few things and he fulfilled them. He said: ‘I have decided to appoint you the leader of mankind.’ ‘And what of my descendants?’ asked Abraham. ‘My covenant,’ said He ‘does not apply to the evil-doers.’ (2:124)
Therefore, when we pray for Aal-e-Ibrahim, it is understood that it only includes those who were true to their lord and fulfilled their pacts and covenants with the Lord. This does not include Jews of today’s time. Since Aal-e-Ibrahim were given special status of Shahdah, first Bani-Israel and later it was given to Bani-Ismael. Therefore, Prayer is only for the pious ones both among the progeny of Prophet Abraham (sws) and of Prophet Muhammad (sws), specifically those who fulfilled their duty of Shahdah.
Actually saying peace on Prophet Abraham (sws) and His progeny covers it all but the reason I think that Prophet Muhammad (sws) and His Progeny are mentioned separately has some literary and historical significance.Prophet Abraham (sws) hold a special status of Imamat while Prophet Muhammad (sws) hold the special status of culminating the Abrahamic tradition to its final form till the day of judgement. Therefore, mentioning of both the start and the end separately covers the whole of the second phase of prophethood beautifully.
Secondly, there is no harm in praying for anyone (whether Muslim or Non-Muslim), Allah will only accept those prayers and give affect to them according to His law of repentance and forgiveness.