I agree, but not even all Nexus phones get upgrades to the latest version of Android.
The Nexus One was released on January 5, 2010. It won't get an upgrade to ICS. Apple's iPhone 3GS was released on June 19, 2009. The latest version of iOS, 5.0.1, gets automatically pushed to it, over the air. It works great, even though the iPhone 3GS is a 2,5 year old model.
That's in stark contrast with buying an Android phone, where models go out of style in a matter of weeks, not years.
The fact remains that Apple consistently provides 2-3 years of updates, for their phones, whereas even new Google-branded Nexus phones are in some cases getting cut out of updates in less than one year.
I think though, that there has to be real push back against the rooting/warranty policies. If I take my car to an independent mechanic, it does not void the warranty. If I hire an HVAC contractor to fix my air conditioner, it does not void the warranty.
If Samsung, et. al., can point to legitimate ways in which a rooted/modded phone can break the phone irreparably, what that tells me is that's an indication of poor design on their part. As consumers we should expect they fix that, not make third party mods difficult.
Even the 4.0.3 source drop for the Galaxy Nexus was awkward because half way through it Google had to stop and go get terms to release updates to the proprietary drivers for their own Nexus device. From my limited understanding, if you want to build a (not cheap, but... affordably, expensively cheap) phone today, there aren't exactly open-firmware hardware choices.
The only way to physically damage the phone is to do some of the (inane) extreme overclocking. Not sure what they can do about that except do more at a hardware level to set caps on that sort of thing. I still suspect the reluctance for rooting/roming is from the carriers (tethering and support primarily). This seems to be backed up by the fact that at least one of Motorola's new phone has an unlocked bootloader everywhere except the United States.
Further, manufacturers have no incentive to upgrade your software because they're already adapting their changing custom code to their NEXT device that they'll launch 2 weeks later as a "sequel".
But, we've all heard this before. Not all Android devices are built the same, not all the software builds are the same. Many devices are more "open" than others, and some models (read, Nexus line) get timely updates.
I don't think it's unreasonable to compare Nexus vs. iPhone and leave many of the other Android phones in a separate class. As an Android user, that really doesn't bother me.