Aquí está la documentación para el método protegido:

/** Converts jmusic score data into a MIDI Sequence */
protected  javax.sound.midi.Sequence scoreToSeq(Score score)

E hice esta pequeña clase para extender la clase de la que proviene el método scoreToSeq:

public class MidiSequence extends MidiSynth{

    public Sequence getSequence(Score score){
        MidiSynth synth = new MidiSynth();
        Sequence sequence = null;
        try
        {
                    // Here I get the error saying that the method has
                    // protected access in MidiSynth
            sequence = synth.scoreToSeq(score);

        }
        catch (InvalidMidiDataException e)
        {
            /*
             *  In case of an exception, we dump the exception
             *  including the stack trace to the console.
             *  Then, we exit the program.
             */
            e.printStackTrace();
            System.exit(1);
        }

        return sequence;

    }
}