This is really a reflection of the TV show version of Alliser Thorne as the book version is a bit different. I do respect that Thorne is a very well-written character, but his semi-evil just makes you hate this guy with a passion. We first notice him when Jon Snow is a recruit at the Night's Watch, as he berates the newbies for being green and weak. Many might not realize why Alliser hates Jon with a passion but Thorne was sent to the wall at the end of Robert's Rebellion. He was a knight in the Crowlands that fought for House Targaryen, and was given the choice of death or the Night's Watch by Tywin Lannister. The Starks were partly responsible for the loss of his freedom (by winning the war) even though he still retained the honor of knighthood. When Ned Stark is executed, he mocks Jon about it in hopes that Jon would try to attack him which he does. While Thorne had hoped to see Jon Snow hanged, Lord Commander Jeor Mormont is far more merciful and lets him off pretty easy.
Mormont sends Thorne to King's Landing soon after to separate the two as he was to ask the Iron Throne for more men for the Night's Watch. We all kind of forget about him until Jon returns from Beyond the Wall and he is eager to see Jon hanged for betrayal even though Jon was following Qhorin Halfhand's advice to spy on Mance Rayder. Luckily enough believe Jon and he is set free. The two drop their differences for awhile at the Battle at Castle Black against the Wildlings. But when Jon Snow is elected to be the new Lord Commander things get worse. Even though Jon names Thorne as First Ranger in respect to his service to the Night's Watch, he remained a vocal critic in Jon's sympathies with the Free-Folk.
Up to the point where he murders Jon Snow along with others saying it was "For the Watch". He tries to take command and suppress those who were loyal to Jon. When the Wildlings take over, they lock him up. When Jon Snow is resurrected, he hangs Ser Alliser and the other mutineers. While most of us hated Olly more, I was glad to see Jon get his revenge. Ironically Thorne fought for the Targaryens to keep the Iron Throne, and he ended up wishing the worst on Jon who is most likely the best heir to the Iron Thorne given that Rhaegar Targaryen married Lyanna Stark.