1) Co-ownership rocks (except when it doesn't). Communities can feel great ownership over a site and its functionality. They work around a site's idiosyncracies and learn from force of habit how to make best use of said site on their own terms. No matter if the site's design is less than appealing, if a community feels ownership over it (like an unattractive baby), they'll perceive it beautiful since it's their own. Open discussion forums, blogs (w/ comments allowed), and user-empowerment (rankings, reviews, networks, etc) are great tools to cement co-ownership with users. Co-ownership is fantastic in terms of generating word-of-mouth marketing and deep customer loyalty. But with that, the expectations of the community are heightened. Co-ownership, whether real or perceived, generates a lot of passion...
2) Vet, vet, vet. If you're an owner of a site, you'd probably prefer changes to said site, whether product, design or policy, be something you can directly influence. If changes are made without involving community members (especially if they're the most vocal members), a user community will feel less empowered, less sense of ownership. This can result in ambivalence to a site (reduced loyalty and word-of-mouth marketing) or worse, antagonistic communities being formed. This is a definite cost to having a community-empowered business model, since the vetting can lengthen development times for product and require multiple reviews of policy decisions.
3) Online communities tend to mirror their offline kin. Once an online community supporting a site has been formed, leaders and influencers arise. Identifying these folks and engaging them in your business decisions and processes are key. Well established communities dont often openly accept radical change since understanding and adjusting to these changes takes a ton of collective work. Just as with any constituency, lobbying for changes with community leaders/influencers can build support across a wide base of users and minimize negative reactions.
4) Never take it personally. The absolute worst reaction to community pushback is to deny, dismiss, patronize or over-react to user concerns. Again, communities are passionate due to sense of ownership. Fully expect strong opinions and strongly-worded expressions of displeasure (and support). Take it on the chin, listen to what's behind the concerns and address them (or at least take them into consideration) as openly and publically as possible.