There is a phenomenon regarding guitar pickups called "magnetic interference." This is where the magnetic field generated by the pickup actually impedes the vibration of the string, causing a dull, lifeless sound. Generally you want to get the pickups close enough for good output, but not so close as to choke the string. Fender recommends around 5/64" clearance from the top of the pole piece to the bottom of the string fretted at the last fret. You can check this with automotive-type feeler gauges.