You are just calculating the total for row 0.
Try this:
private void btnTotalMouseClicked(java.awt.event.MouseEvent evt) {
String userTotal = "";
String userBonus = "";
int bonus = 1000;
for(int i=0; i < rowNumber; i++){
int total = (points[i][0] + points[i][1] + points[i][2] + points[i][3]);
userTotal += name[i][0] + "'s Total Points are: " + total + "\n";
userBonus += name[i][0] + "'s Total Points are: " + total + " Bonus: " + bonus + "\n";
if(total > 5000){
outPut.setText(userBonus);
}else{
outPut.setText(userTotal);
}
}
}
}