I'm conflicted about Axel to,but for a totally different reason.I'm trying to decide if I still like him are not after the cold, evil, and cowardly displays of murder he did in the Re:com cut-scenes.
But to answer your question I don't think Axel or the rest of the Organization are good or bad,but both.
That is why they are Twilight after all.Anyway, don't delude yourself into thinking Axel is completely good.Like many have already posted Axel is looking out for number one always and foremost.
In Re: Com he ignored Namine's escape not because it was the right thing to do,but strictly for his own amusement even saying namine,sora,murluxia,vexen it's time you give me one hell of a show.
Vexen tries to tell Sora of what Marluxia(the real traitor) was doing to him and he was about to reveal Roxas to him as well and Axel kills him to shut him up while smiling sadistically.
He tells Zexion that it's more fun to watch the expliots of Sora then to save him then tells the replica to drain him,then proceeds to tell the replica right after to go fight the real riku so he can amuse himself with his death also thus making Zexion's death pointless.
Marluxia makes Namine appear in front of him,and Axel says he'll even go through her to get to him,and then they can spend time in the void together.
in KH2
Axel kidnaps Kairi
Saix warns Sora that Axel would stop at nothing to turn him into a heartless,and Axel confirms this in the novel when Riku warns him about it.
While it's true that Axel does have some affection for Roxas a large part of that friendship was what Roxas's proximity did for him. Everything he did in Castle Oblivion,and his dying words"He made me feel like I had a heart" confirms this.
Axel kills his fellow members because of the threat that through them his gravy train to feeling like a complete human again might be revealed. Then when he can't stop Roxas from joining with Sora he completely betrays them,and sets his sights on Sora since his gravy train is inside of him now.He destroys himself because he was saving Roxas his fix on feeling like he had a heart,and in essence it saved Sora don't delude yourself in to thinking otherwise.
In Axel's journal entry it basically says Axel is a back stabbing hypocrite without actually saying the words.
All that's really keeping Axel from being dumped as one of my favorites now is his friendship with Roxas,and to be honest if Axel was real I wouldn't want him as a friend because I'll be to scared of when the knife' s about to make impact with my back.