I once read (I believe in the liner notes to her greatest hits CD) that the song was her protest about changes dictated by the record companies. She wrote songs and wanted to record them a certain way but was not allowed to release them the way she wanted.

Fittingly, the title of the song was "Look What They Done to My Song, Ma" but the record company did not allow that due to it being grammatically incorrect. The title was therefore changed to "What Have They Done to My Song, Ma"
That is how I remember it anyway.