Something I've struggled with a lot as a serious photographer. Glad to see this topic come up.
I borrowed a buddy's fstop bag for a 10 mile day hike last year... I didn't like it at all. limited space for non-photo gear, uncomfortable compared to regular day packs, and just feels more "stiff" overall (if that makes sense).
I've come to the conclusion (for myself at least) that my Osprey day-pack or Osprey Atmos65 multi-night pack is MUCH more comfortable to wear in the field. I normally carry a Canon 1ds3, 2 lenses, and a tripod. I have NEVER had an issue with them sitting in a regular pack. The inconvenience of access is outweighed by comfort for me.
In my day pack, I wrap my gear in bath-towels for shock absorption. In my overnight pack I actually wrap photo gear in extra clothes/layers to save weight. I keep the gear in the center of my pack... over my sleeping bag and under the tent fly. This helps for added padding. My tripod is normally strapped to the back. I've taken a few slips and falls over the years, but have never had gear damaged during so.
An added tip... putting camera bodies/lenses in ziplock bags before putting them in your pack can be a great added sense of security if you know you have sketchy creek crossings during your hike
Also, I keep a few hand-warmers in my pack to keep camera batteries warm or tripod legs thawed during winter excursions.