By transforming 60 hertz AC at 120 volts down to 12 volts the transformer acts as an electromagnet 60 times per second. This causes the transformer to vibrate. Now if the transformer is not tightly mounted it may make a louder noise. Sometimes, the manufacturer may isolate the transformer with rubber gromets to minimize the sound.
You could always re-eingineer the manufacturers design to improve the quietness (lower the noise output).
Also, keep in mind that the transformer makes more noise when shorted-out because it has to work harder. Also, the more lights you hook-up the harder it will have to work.
Your doorbell also uses a low voltage transformer. They often mount it in the basement next to a light fixture. Go see if it hums. Keep in mind that it isn't doing any work until the doorbell rings.