I don't think it is reputation the manufacturers are concerned about. They care about money before anything else. Yes, reputation can affect sales (ever so slightly), but that is a secondary effect. A primary effect is customer support. And, it is sooooo easy to refuse support for a rooted device.
Yes, there are half-wits who have no clue what they are doing and who break their devices ... but these will find a way to root and screw up anyways.
On the other side, if the manufacturers and Google would not constantly screw up and give their users more choices/freedom, there would be fe