Reputation for Indie (not affiliated with any superpower) minor factions affects that minor faction only - there is no flow-on effect like that for superpower-affiliated factions.
Doing missions for Indie factions does not help your Superpower rank, unless the "destination" faction happens to be Superpower-affiliated. However, doing missions for Indie factions does not hurt your Superpower ranking either. The Superpowers don't punish you for working for the Indies. If local politics does not interest you, then it is always advisable to quickly check through all the mission offerings, to see if anyone else is offering courier or cargo missions to the exact same destination a ranking mission is taking you to. Why not? It's free money, for doing something you were going to be doing anyway.
If you are working in the same region of space all the time, rather than living a more nomadic lifestyle, then you will probably find your reputation with the Indies will trend upwards in any event, since an Indie minor faction will often be the target faction for any Superpower missions you undertake and most missions have a positive, rather than negative impact on the receiving faction. I seem to be at least Cordial and more often am Friendly or Allied with every non-Anarchy faction within 20 LY of my "home" system, even though I actively support only the Fed and Imp factions. And the "non-Anarchy" qualifier in the previous sentence is only there because I actively avoid doing missions that help Anarchies.