rear caps on in my camera case (storage) but off in my shoulder bag when I'm shooting. the shoulder bag is padded on the bottom and I put a lens cloth at the bottom of each slot, so the rear of the lens is protected from impact and scratches.
Rear and front caps off, no filters, no hoods (I use my hand for flare protection). All lenses go on my Steroid Belt in the Skin pouches. Only times I use caps are if I'm in a dusty environment like at a construction site.
I store them with caps on, but once they come out for a shoot the hoods are on and caps are off. Sometimes I'll put a rear cap back on when switching. No filters.
no front caps except on my fisheye, have filters on everything that needs it....55 macro and 50 1.8 dont get them b/c the front elements are recessed so far.....lenses all live in my thinktank belt system, i even store some lenses ass end down in the pouch, mainly my 17-55, and used to be my 70-200 vr 1 till i sold it....i know it's risky pulling a lens out hood first, but i've never dropped one (knock on wood!!)
I have rear caps on my Leica lenses. 2 reasons. Firstly I store my lenses in my belt system with two caps taped together because the lenses are so small. Secondly because the M9 is the greatest dust magnet of all time.
For my AF stuff I don't use caps during the day but have them in the bag for storage. Hoods are on all the time,
No caps front or rear while shooting, just hoods up front. Rear caps back on when stored between shoots. I have no clue where most of my front caps are.
I keep all caps on while the lenses are in the bag for storage or transportation.
During the day, I have hoods, a filter or both on all my lenses:
14 2.8L II - no filter or rear cap
24-70 - just an UV filter (the hood is too big and obtrusive).
24 1.4 II - UV + hood
50 1.2L - hood (the filters create some flare that I am not too happy about)
100 macro: UV filter
135 2.0L : sometimes just UV filter (hood too big), sometimes hood + filter or for those times when I want some flare in the images without the circular reflections from the filter, I remove the filter.
I use a waist belt with some lens holders. Sometimes I have two cameras on me (one over the neck and one over my right shoulder). I have no rear caps for the lenses that go inside those. It usually takes me a few seconds to switch a lens.