You probably don’t have the pistol equipped as your secondary weapon. Press the R2 button and make sure the pistol is the item selected on the right.
Alternately, it could be because you’re out of ammunition, although the game should give you a pop-up scolding you about that if that does ever happen. (Which it shouldn’t if you’re being a responsible assassin and looting all the bodies)
Are you holding the left trigger to aim first? If you are and it’s still not shooting, that means you’re not in range. Get closer to your target and it will shoot.
No, it’s in the little picture. And yes, I’m holding the left trigger. Although sometimes when I stop doing that I do shoot. At the ground.
Is the thing you want to shoot highlighted with a white outline? If it’s not, you can’t shoot it, period. The game won’t let you just shoot wherever you want, you’ve got to have a target selected. If the target is close enough, the game will auto-highlight it for you, and all you have to do is press Y. If the target isn’t close, but isn’t quite out of range, you can select it by holding Left Trigger and putting the cursor on it. If it gets highlighted, go ahead and shoot with Y.
You’ll also know it’s OK to shoot, because the ranged weapon icon on the lower right will switch from dark blue to light blue. And I’m pretty sure you have to release Y before you actually shoot - supposedly aiming longer gives you a better shot.
Is it the mission where you first learn to shoot a pistol and musket? I remember that one being a pain in the ass too.
In Assassin’s Creed: Brotherhood, I assassinated many patches of ground and/or random buildings with my crossbow. :o
I found the biggest pain in the ass so far was trying to shoot the powder wagons when you’re chasing the general on horseback (for full sync). You have little margin of error to fall behind the general before you desync. You have to time your shot just right. Too early and you won’t shoot and then you have to release the shooting button and try again which brings you too late in which case you ride past the thing. Also, the game sometimes tries to line you up with other soldiers rather than the powder wagons. Also if you’re too close to them when they go off they can at best slow your horse down and at worst kill you or it. Oh, and you have to reload between shots with enough time to get the next one in range at the right time, and the game doesn’t always seem to want to reload when you tell it too.
Yeah, I hated that part of it.
Oh my god you ridiculous little shit STOP CLIMBING ON THE FUCKING TABLES WHEN I’M TELLING YOU TO RUN! Yeah you hit A so he then climbs on the NEXT TABLE and wonders why they’re stabbing your feet. Escaping is really, really frustrating for me.
And why isn’t there a difficulty level on the game?
And now to add insult to injury I’m lost (in the real world, so there’s no minimap.) Went exploring in the temple and now I’m totally stuck somewhere on the same six staircases. Been running around for twenty minutes now.
Ha, yeah that shit gets so annoying. I loved how Ubisoft was trumpeting how all that control crap was fixed.
I’m with you on this one. For God’s sake please stop sticking to everything; or assuming I want to jump onto something.
God help you on a mission where you have to ride a horse quickly, and you barely miss the tiny path, but instead step up on a rock that horse can’t jump off from even though it’s only a 1 foot drop off.
Oh God, that mission where you have to chase the soldiers down before they get to the camp? Talk about frustrating. That horse comes to a complete stop for what feels like no reason so many times.
No kidding. I can’t tell you how many times that happened to me. It’s especially worse because the checkpoints on those types of missions were so few and goddamned far between. Urgh!
Well, I gone as far as I care to go. I’ve almost completed it all except the “Encyclopedia of the Common Man” mission; which I screwed up on evidently and won’t be able to complete unless I start over. 
Also I am not able to win a game of Fanorona in my homestead. I’ve apparently have a learning disability when comes to that game. I can be up 7 or 8 stones, to my opponents 3 and I couldn’t win.
I really like Haytham! Why can’t I go hang with Haytham for the rest of this game? Connor’s such a little dick.
I really liked him, too. Connor’s more fun to fight with, but Haytham’s easily a better character.
Haytham is also way, way hotter.
Just sayin’.
I almost feel like they designed the game to be about Haytham at first, and then decided that people wouldn’t accept a game based around a Templar.
ETA: Though I would have loved a game where it starts out the way it did, and then an older Haytham slowly decides that the Assassins are better.
Yeah, especially since I find Connor incredibly boring so far, and I’m though Chapter 8 (the one where you kill the guy who’s just in it for the money after spending the entire chapter in storyline missions by force).
In fact, I find I don’t care about any of the personas in this game. As opposed to Ezio, who I actually thought was one of the most complex protagonists in a game.
And the voice actor for Connor can’t act worth a damn.
“I am… so… Indian. How. You can tell because I am unable to use contractions.”
I care about my little homestead people! I am such a girl. I want them to be very happy and have tons of babies and make me a lot of money. I’ve enjoyed those missions way more than anything else! (I do quite like the naval missions also but have been spreading them out a lot. It’s a fun little interlude.) I haven’t run into the Founding Fathers for awhile either (took some time off from story missions, honestly) but I really liked them - they were all very individual and I bought them as people. Like how Paul Revere never had his shirt tucked all the way in and was a jovial little dick.
Connor, on the other hand, is a snoooze. And he keeps letting people stab him in the ankles while he tries to climb things you can’t climb. Dumbass.