After a while, you realize there are no clear cut completely good guys or bad guys (though some characters are more good/bad than others).
Hell, the whole premise is based on the fact that all this terrible stuff goes down 15 years after the good guys won!
The story may be soaked in blood, but none of the violence is glamorized or portrayed as positive. It's a tragedy on a human scale.
On the other hand, book one is far and away the best and the last one really wasn't all that good IMO. So who knows where this adaptation will go, or where the future of the series lies at all.
Another thought on episode 3: When Ned mets Jaime in the throne room, he had a chance to make a small amount of peace between them. Jaime is being almost conciliatory. I got the sense they could never be friends of course, but Ned makes it worse by being so completely honorable and forthright. Completely seals his own fate.