Import Certificate to Trusted Root but not to Personal [Command Line]

Look at the documentation of certutil.exe and -addstore option.

I tried

certutil -addstore "Root" "c:\cacert.cer"

and it worked well (meaning The certificate landed in Trusted Root of LocalMachine store).

EDIT:

If there are multiple certificates in a pfx file (key + corresponding certificate and a CA certificate) then this command worked well for me:

certutil -importpfx c:\somepfx.pfx

EDIT2:

To import CA certificate to Intermediate Certification Authorities store run following command

certutil -addstore "CA" "c:\intermediate_cacert.cer"