This misunderstanding, IMO, is the cause of some of the frustration over the trail use. The bicyclists think the pedestrians are supposed to be off on the dirt on the left side of the trail, which is not so. The city developed the paved trails for all to use.
I think it is good practice to run on the left side whenever possible, and I run on the shoulder when it is available, flat, and not full of rocks pot holes. I often switch left to right on winding sections, as I've almost been hit head-on by speeding bikers hugging the turns.
I do ride my bike on the trails as well, and I'm not going fast enough to be bothered by pedestrians. My only issues have come from dogs which are off-leash or when the leash is too long.
I will not walk on the dirt or run in the dirt, in my running shoes. I use those trails to exercise and not have to compete with car fumes. I do not like getting little rocks and sand in my running shoes.
however, when I plan on running on dirt trails, I wear the right pair of shoes (nice traction).