One problem with zoom lenses, where the focal distance is changed with a turning motion rather than push/pull, is that there is no way to indicate visually what the depth of field is. Since I only use a pair of such zooms, I have that problem all the time, so I always have the AF on, at least for aircraft photography. For other kinds of photos, I occasionally switch it off, but generally it works so well I keep it on.
My main aircraft photography rig is a Canon EOS II (50 in Europe) with a Canon USM 100-300mm lens. It has never failed to focus properly and quite fast on the subject, except on a few instances when I forgot to switch the AF back on when I was in a hurry
. As a bonus, the Elan II has 3 AF modes, one of which is 'AF Servo', which, as long as you have the shutter button halfway down, continually adjusts the focus if the subject is moving towards or away from you. A bit hard on battery life I suppose, but it works very well. My other camera, an EOS 500N, does not have this feature, and the focus is essentially locked unless you release the shutter button and push it halfway again.
With these USM lenses, I have never had any problems focusing through glass, including double or triple-pane, tinted and non. Don't ask me why, but it works.
The only thing you should feel when shooting a terrorist: Recoil.