The article you cite doesn't seem to really agree with you:
> So why the global obsession with the one species that makes honey? For one, honey bees have hives, which makes them easy to keep and transfer en masse. For another, some native bees are picky about which flowers they prefer and where they live. As a result, commercial pollination is almost wholly dependant on honey bees.
> ...The goal of all this work is not to replace honey bees, but to pinpoint which native bees are effective, what they can offer and how to lure them into visiting and pollinating.
From what the article describes, the honey bee is uniquely suited for the niche we need it for, and there is no other species even remotely as well adapted -- though they're trying to figure out if any other species could be made to work in some lesser capacity.
So it doesn't seem that native species are underappreciated -- just that there are very good reasons we use the honeybee instead.