Bottle jacks are harder to move in and out under a vehicle and they require more space between the floor and the bottom of the vehicle for clearance. You can't even begin to fit a bottle jack under most average size vehicles as there isn't enough room under the frame.
Also, as you raise a vehicle up there is movement since the vehicle raises in an arc motion. A bottle jack is stationary and therefore it could result in the vehicle slipping off of the lift point or the jack tipping. Floor jacks often have wheels and can slide to prevent any movement.
Add to this that floor jacks have longer handles allowing for faster jacking action and that they generally have a larger range of motion (a 5" tall floor jack might have 15" or more of lifting height for example)... it just seems they are better for working on vehicles.
Bottle jacks have their purposes - but it is generally on heavier equipment or stationary uses such as raising a building or acting as temporary support for a structure. Floor jacks are just better and more efficient for working on the average vehicle, so that is likely why you tend to see more of them in garages.
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