I backpack a lot, and my feet used to kill me with plantar facitis, until I thought I was going to have to give up backpacking. Two things seem to have solved the problem: get a boot with plenty of room in the toe box for my toes to spread out, and good arch supports so my plantar fascia doesn't get stretched out. Jake's remedy of wearing no shoes when possible would be similar to getting boots with plenty of room in the toe box, I think.
My latest pair of boots are Meindls, which you evidently have also, which work very well. The Meindl's also seem to have soft padding behind my heel, which helps with a bone spur I have back there. I have also had success with Keens, but they rarely seem to have a really high quality all leather boot. They recently came out with one, the Liberty Ridge, which I thought would be good, but has a hard spot behind the heel that aggravated my bone spur, so now is relegated to yard work and the archery range.
Sorry, but don't have any recommendations on rubber boots.