I don't care that much about locked bootloaders, my main reason for rooting is improved speed and battery life along with a few programs I don't use that often.
Still, it's nice to know being rooted you can always get the most out of your phone and extend its life (the latter probably why they are locking bootloaders).
But I still say rooting is such a small % of users that these companies stand to benefit much more than the bottom line is hurt. You're rooting community is a free bunch of beta testers that help to improve your product.
Personally I think it all comes back to money. As I've said before, the hardware is becoming increasingly commoditized and it will be software and UI that ultimately differentiates service providers and manufacturers. They don't like the idea of hackers and developers bringing rooted phones for free what they intend to monetize - stuff like wireless tether, home launchers and themes. A much more user-friendly version of Locale or Tasker integrated into the phone hardware/software could be a powerful point of differentiation for the manufacturer.
This is what we've seen with MS in the past not sharing some of its program modules, right? That prevents people from replicating or doing some things MS can create and sell. Same thing here. If, for example, developers can't fully control the FM chip or whatever, then Moto can develop and sell and exclusive FM transmitter app for its phones.
No, it's not good for the users. But it's a constant battle between these companies trying to make a buck and users wanting stuff for free. So long as competition breeds choice I can't really complain. Problem is with more phones being locked down there will be less incentive for developers to create rooted apps.
Something else to consider is the rooted community is never satisfied - just look at the love/hate relationship with new roms. I tell everyone I meet with a Droid they need to root. From a manufacturer's perspective, rooting becoming a significant portion of users can adversely affect perceptions of quality that they have no control over.