This is something that I think you're always going to run up against when you have to come up with something creative for a client. I run into this sometimes when I'm producing a record for an artist. If they're funding their own project, which means they're the ones paying me, I need to take that into consideration.
You get more leeway in dealing with a client if it's your own business. But if you're working for a business owner on a client's project, it's more complicated. Sometimes you do just have to shut up and collect a check. If the reputation of your own business is at stake, maybe you can take a stand on what kind of work you'll do, and what you won't.
As for web design? It's not my field. But if it were, I would make a point of showing clients some successful sites, and what it is that makes them great. School them on the features so that they're at least educated on the process. And if they still want crap...then they want crap.