I'm rather tired of hearing this assertion across various threads in this forum. So the story goes: Ned Stark was doubtlessly a good and honorable man, but was too honorable (to the point of naivety) to play the game of thrones, and thus was defeated because of the lack of his political skills.
I could go into a lengthy tirade about all of the flaws in approaching any realistic scenario with Realpolitik, but it's unnecessary.
Eddard was actually a fairly crafty politician, as seen by his actions as Hand. He manipulated the composure of Robert's will in order to oust the Lannisters from the throne, then bought off the goldcloaks to prevent a coup d'etat. These are not the actions of a man "too naive to be a politician". It's in no way a bad plan. The failure was that he trusted Petyr Baelish, but this was on the advice of Catelyn, who was his friend from childhood. Eddard made a calculated risk that Littlefinger would more likely befriend the Starks than the Lannisters, since he knew that Petyr knew that the Starks would not betray an ally, whilst the Lannisters would. Cersei made the same risk, as well. If Petyr had decided to betray her instead, Cersei's entire plan would have been foiled.
While I'm on this subject, can we talk about how bad Cersei's plan was? She has until Robert returns from the hunt before he and Eddard put the Lannisters to the sword for high treason, and her best plan was... to get him drunk and hope the boar fatally wounds him. The fact that this worked out at all is amazing. Also, with the revelation that Jon Arryn was killed by Lysa and not by the Lannister conspiracy makes this whole plot even more contrived. Was Cersei hoping that a hunt was going to kill Robert when Jon finally realized that Joffrey was a bastard, as well?
So basically, Eddard's failing was two things: one, that Cersei's ridiculous plan managed to succeed at all; and two, that Petyr (who, from any perspective beyond his inner thoughts, had more reason to ally with the Starks than the Lannisters) betrayed him and had the goldcloaks side with Cersei and Joffrey. How is this "naivety"? He didn't have a bad plan. There was really no better plan available. He was not held back by his honor and sense of justice.
The one thing (only in retrospect, though) that Eddard could have done instead is cut Littlefinger out of the equation entirely, and use his authority as Hand to replace Janos Slynt with a northman (or at least somebody more trustworthy). I'm not quite sure how that would have gone down, though.