Tobi was well aware of Itachi's true motive for joining Akatsuki. He knew that Itachi massacred his entire clan only for the village's sake.
Then why did he let Itachi join the Akatsuki?
He was also aware that Itachi was trying to protect the leaf village from Akatsuki. So my next question is
Why didn't he get rid of Itachi at least after they start to capture the tailed beasts?
He let him stay because a lot members of the organization had their own motives and knew they would betray the overall effort at some point or another. They are all missing nins which means loyalty to an organization was clearly not on the top of their list. Many were even there just to spy or further their own goals. It didn't matter to him as long as he can use them to accomplish immediate goals. And everyone of them thought they would eventually outsmart, control or win over the others as they are all excellent ninjas.
He also didn't think Itachi knew as much as he did or was good as he was (a testiment to how good a ninja he was). Also he liked the idea of having extra Sharingans hanging around in case he needed them.
There is a very similar thread on Narutobase: Itachi and Akatsuki
Slightly edited the posts here and there.
Then why did he let Itachi join the Akatsuki?
Tobi gained a lot from Itachi- help with tailed beasts, stalled Gaara rescue team, help with killing off the Uchiha clan while keeping his identity secret (Chapter 400,Page 9), let Sasuke be so that he can take care of Itachi as per his plan later only to use him as a pawn after Itachi dies, and once that's done he can attack Konoha without warning and seal the Kyuubi last.
Itachi was an eyesore for Tobi's plans and he never wanted Sasuke at first but when Nagato died he needed some one to sync with Gedo Mazo (Chapter 453, Page 17), so he recruied sasuke as he was short on members.
Itachi was happy since village was safe and also he was keeping eye on the Akatsuki. We have seen this as Konoha was attacked by Pain after Itachi died and not before that so it make sense.
Thread on Narutobase discussing why Itachi couldn't kill Tobi:Establishing why Itachi could never kill Obito once and for all
Why didn't he get rid of Itachi at least after they start to capture the tailed beasts?
Itachi was a Leaf's spy, but he was nevertheless a useful asset to Akatsuki. Add to this the fact that Itachi never had the chance to share any intel he gathered with Konoha, nor did he manage to interfere in Akatsuki's plans at any point and you get an ALMOST full picture. The last reason Tobi kept Itachi alive was because of Sasuke. As we know, Itachi wasn't willing to cooperate with Tobi really. But, thanks to Itachi's death by the hands of Sasuke, Tobi was able to persuade Sasuke into joining him. That's how he gained a powerful tool (because an ally is a wrong word here), especially after Sasuke got Eternal Mangekyo Sharingan. In other words, killing Itachi would be a complete waste. Even if Itachi was stronger than Obito, Obito could have get ridden of him at any point he wanted. He was pulling the strings behind the whole organization, ordering even Nagato around. If he wanted to, he could have simply ordered Nagato to do the job. As you can see, no matter the individual strength of Obito, he could have got ridden of Itachi anytime he wished. He didn't - not because he was too weak, but for the reasons stated a point above.
Because he wanted Sasuke to kill him and awaken his powers and control Sasuke after that because he is easily brainwashed and anger revenge driven.
Well even if Obito did get rid of Itachi he would have had a hard time since it is shown in one of the anime movies that Obito says to Itachi that he was a nuisance as always since he could have killed obito with his black flames the eternal flames of sharingan. and also Obito would have lost the advantage to throw sauske in even more darkness and use him against naruto
Firstly, Obito is stronger than Itachi and we all know that! Susano isn't able to defeat someone who has Kamui, even tough Obito has only one eye, He still stronger than itachi, and Kakashi become stronger than Itachi in Naruto Shippuden! of course, Itachi has deadly jutsu, but someone like Kakashi who knows everything about uchiha, I don't think izanagi would be a useful jutsu against him! All he's gonna do is waiting for him to get back to life and kill him another time! Anyway, what I wanna say is Obito used Itachi, and he wasn't afraid of him at all! if he planned to do something he will kill him! Guys, I'm not a fan of any of them but, Obito is stronger than Itachi, and if he didn't give his eye to Kakashi, kakashi wasn't even going to be in the list! So, Obito used itachi, like when Pain defeated orochimaru so easily, and forced him to join and Pain tells sasori that if orochimaru did something i'll deal with him personally! Pain treated orochimaru as a kid, while obito did the same thing but, not that easy at least obito was aware of itachi a little because he's stronger than itachi, but not to the point where he'll defeat him easily! That's why he tells him to join Akatsuki
