The intercept is equal to the E(R) for a stock that has fundamental factors sensitivities equal to the market-wide averages. This will be the E(R) for a stock with the average fundamental factors (P/E, P/B, EPS, or whatever). Since the FFM uses standardized sensitivities and not regression slopes:
Stock avg. Sensitivity = (P/E - P/E avg) / Sigma avg
P/E = P/E avg, so the Standardized sensitivity = 0 (ie zero standard deviations from the norm).
Does that make sense?