Following from #3090 there's no support for Authorization: Basic ... with marathon, which is what non DC/OS installs use.

Part of the auth_token changes mention this: 2aba238

Existing configuration files that use the bearer token will no longer work. More work is required to make this backwards compatible.

Even before the auth_token[_file] changes this wouldn't have worked.

https://github.com/prometheus/prometheus/blob/v2.2.1/discovery/marathon/marathon.go#L300-L305