There aren't necessarily serious arguments against encrypting DNS but there are serious arguments against implementing it at the individual application level in

There aren't necessarily serious arguments against encrypting DNS but there are serious arguments against implementing it at the individual application level instead of honoring the system DNS settings configured by the system owner. System owners are now going to have to be concerned about configuring and locking down DNS settings in multiple locations. Troubleshooting issues caused by DNS problems will be more difficult as different applications may use different DNS settings. Filters such as child protection filters are more difficult not only on the ISP level but at the home and corporate network level also. I fear the reaction to this is going to be more https interception on corporate networks as traditional DNS interception and filtering becomes less useful.