The whole Uchiha clan rebellion explanation does not make sense, no matter how you put it. I'll explain why:
1) The Uchiha clan was never very large. At most, it was maybe 100-200 people. Of those, only about 2/3rds, IF THAT, would be capable of participating in the coup. The elderly, the young (particularly genin), and those who are very out of practice would not be helpful in a coup.
2) Konoha's shinobi force of Chunin level or above numbers somewhere between 10,000-20,000 people.
3) The Hokage is a powerful guy with powerful summons. He's also very well loved by the village.
4) The ANBU force are elite, and loyal to the Hokage. Nearly all of the jounin are as well.
5) The Uchiha Clan was all located in a single place in Konoha.
6) The Hokage and the elders knew about the coup, and since Hiruzen tried to negotiate with the Uchiha, we know that the Uchiha knew that the gig was up.
7) Because of number 6, the Uchiha leaders would know that the Hokage could have most of ANBU, and even some jounin, surrounding the Uchiha district at any given moment, ready to move in and neutralize the threat. For the Uchiha leadership to walk away from the negotiating table in any way (or to not go there at all), they would have to be unbelievably stupid and insane.
8) Also because of 6, subduing the ringleaders of the coup would be relatively easy and avoid most unnecessary casualties. The threat of "we can kill all of you at any time" tends to work pretty well in that situation. Subduing the clan as a whole would not be that difficult either.
9) Itachi, ITACHI of all people, had no qualms about following Danzo's "kill them all" order, despite it not coming from the Hokage. If it meant not murdering children, his lover, innocent old people, his mother, and his best friend, such obvious alternative options would have given him pause. Also, no other ANBU or jounin tried to stop him.
10) The Uchiha already HAD tons of power and elevated status. The only thing they didn't have was an Uchiha Hokage, but there was no discrimination against them (Minato was not Senju, nor was Hiruzen, and nor was Orochimaru, who was considered as a candidate). There would be very little incentive to risk everything.
11) Itachi brutally mind-raped Sasuke twice, and drove him to insanity, abandoning his friends and his village, and encouraged him to murder his best friend. Does that sound like a loving older brother to you?
12) Even if the Uchiha clan was larger than we can reasonably guess, keep in mind that a single 13-year old ANBU captain managed to kill ALL OF THEM in a single night, without any of them putting up a significant fight. If that was possible, then imagine what 90% of the ANBU force with many jounin mixed in could do.
13) Itachi's deal with Tobi came from nowhere and—you guessed it—doesn't make sense either. Tobi's power should be capable of crippling Konoha singlehandedly in a single night. Obviously, despite wanting to very badly, he never did. Nor did he ever kidnap Naruto, despite a LOT of evidence that he had the ability to do so. There's obviously some reason why he never did (even long before the Uchiha Massacre), so Itachi's deal does not make sense, even if Tobi had any incentive to keep his end of the bargain. Also, how did Itachi even find out about Tobi, let alone find him?
14) It's not like Danzo to want to exterminate such a powerful kekkei genkai when alternatives exist. Ordering Itachi to spare the children would have made more sense, especially since said children would be easily influenced.
15) Sasuke has every right to want to kill Danzo and the other elders for the Uchiha Massacre. Killing people whom they KNEW were completely innocent, as well as many who could be subdued without killing them, was beyond excessive and monstrous.
