Do I have trouble with them? Not at all...'cause I don't play them. Ba dum tish.
In all seriousness, back when I played console games, console shooters didn't give me -too- much trouble, but I did find the controls more difficult than with PC shooters. For me, analog sticks, for whatever reason, seem to frequently lack the responsiveness and ease of control that a mouse does when moving a first-person crosshair. Now I seldom had as much trouble with over-the-shoulder shooters like RE4 or Dead Space, funnily enough. However I think part of that is due to the mechanics of third person shooters like them. In such games, turning your character in the direction of an approaching or attacking enemy immediately puts your crosshairs/laser sight in the general vicinity of the enemy, so once in aiming mode a little nudging with the analog stick puts your sights on what you want to shoot. With FPS's, it's tougher because your camera controls and aiming controls are often connected. It creates a difficult dichotomy wherein if the controls are too fast and sensitive, you'll overshoot the target constantly but if they're too slow, you'll be laboriously panning the camera while an enemy just outside your peripheral vision runs up and cuts your ear off or takes potshots at you while you slowly turn to the side like an oscillating fan.