That's all as it should be, IMO. The lead single is chosen because it's the most accessible, the most likely to be a hit or at least get people to hear it and maybe buy the album. Or today, when the general masses don't really buy albums anymore, they'd just check out some more songs by the band. Pull Me Under did its job. It got some exposure for the band, and a bunch of people bought the album. Of those, sure, not everyone liked it. But a sale was made and the band was exposed to some new ears.
Years ago, when Queensrÿche had "Silent Lucidity" out, my wife was asking me about it. She was looking for it on our hard drive so she could put it on her iPod, but was confused because she finally found Queensrÿche under Prog Metal. First, she'd never heard of Prog Metal, but she wasn't shocked that I had such a category. But mostly she wondered why I had them filed that way when obviously "Silent Lucidity" was neither Prog nor Metal as far as she could tell. I'm sure a lot of people picked up Empire and were a bit stunned by the rest of the album. Maybe not "Jet City Woman" which was also pretty accessible. My wife likes that one, too.
Same thing with "More Than Words" by Extreme. MTV views were logged, album sales were made, but I'll betcha the rest of the album caught a lot of people by surprise. But again, some people probably latched onto it and became Extreme fans when they otherwise wouldn't have.