Game of Thrones 6.10 "The Winds of Winter" (spoiler alert - season finale)

[Xithras]

229. Hiding Jon's identity was as much about protecting the kingdom as it was about protecting Jon.

Ned Stark was a man of honor, and by his honor codes you go to war when someone kills your family (he went to war when the Targaryens after they killed his father and brother). If Robert Baratheon had known about Jon, he would have demanded that the baby be killed...and even if Robert had wavered due to his friendship, Cirsei and the Lannisters wouldn't have allowed him to be weak when their claim to the throne was being put at risk. Because Ned would have never handed a noble born blood-Stark over to the Iron Throne for execution, the inevitable result would have been a war between the Iron Throne and the North. To make things worse, many houses supported the Targaryens right up until Kings Landing fell and it looked like the family had been exterminated. The existence of a new heir might have caused those houses to rise again against Robert in aid to the north, throwing the entire kingdom into yet another war.

While Ned certainly wasn't pleased with the murder of the Targaryen children, his decision to flee north and hide Jon's identity was an attempt to save the kingdom as much as it was to save his nephews life. I don't think it had much to do with the bloody end that the other Targaryen children were subjected to.