My advice is threefold: One, make sure the boots actually fit. They may simply be a half size too small or too large. Two, keep wearing them. Do some short hikes, and see if you can increase the distance without getting sore feet. Three, replace the factory insoles with something like a pair of Superfeet ($28; www.rei.com). These will often add greater comfort immediately, as perhaps your problem is related more to the curve of your foot against the insole, not the boot's stiffness.
If, however, your boots are just too stiff for you, try this: Put on the boots and find a concrete curb or step with a very solid edge. If you can hook just your toes on the edge and the sole doesn't flex, then maybe they're too stiff. I say "maybe" because at times I've worn boots with full steel shanks, with absolutely zero flex, or close to it. And while they weren't the most comfortable trail boots in the world, they weren't the worst, either.