Gilbert is a classics man, so in a three week race he would hunt for stage wins. Silence-Lotto already has Greg Van Avermart who won the points jersey in the Vuelta last year (Vuelta points jersey not a sprinters jersey like in tdf though, beat Valverde IIRC). And as was already said he rode the Giro so was probably put at the back of the line for tdf.
But the major reason why he's not there is the fact that SIL are supporting Cadel Evans, which is why he's team mostly consists of climbers and a couple of roulers for the flats and TTT