Because of perception. The fact that you even know what rooting means suggests that you are much more technically informed than most users.

For most users, if they do something and the phone breaks, who do they blame? The phone, of course. If they do something to make the phone run slow? It is the phone's fault, of course. So, by restricting access, companies ensure that users wont put a stick in between the spokes of their bike and then yell at the bike for messing up.

This is the same reason why apple doesn't allow external SD cards or removable batteries. Because people will put a sub-standard quality thing in there and then go "stupid iPhone not working right..."

Basically, the calculation is that the company is better off if people get a consistent and working product, and worse off if they are given the opportunity to have the best possible product but also with the possibility that they'll break it. (Also, historically, Microsoft allowed a lot of access and Apple didn't, then Apple made the most popular phone ever with the same philosophy, and then other phone manufacturers copied them).