Here's the documentation for the protected method:
/** Converts jmusic score data into a MIDI Sequence */
protected  javax.sound.midi.Sequence scoreToSeq(Score score)
And I made this little class to extend the class that scoreToSeq method comes from:
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;
    }
}