Did you choose to emulate weak sectors when you burned your disc? If you did, then yes, you will have to have Hide CDR Media enabled whether you play from a burner or a CD-Rom.
If that isn't the case though, then you shouldn't have to have Hide CDR Media enabled.
What burner do you have?
While I don't have SimCity 4, I do have an assortment of Safedisc 2.8 games that I can play just fine from my CD-Rom without Hide CDR Media or Ignore Media type.