El Al is accomodating those Jews who choose not to fly on shabbat. Since El Al is owned by Jewish proprietors, frum (observant) Jews such as myself would not fly El Al if they knew the airline was committing a transgression of Jewish, biblical matter. Consequently resulting in the loss of thousands of currently loyal customers.

If you want to fly to Israel on shabbos, you have a myriad of other options:
TLV Direct: Delta (ATL), Continental (EWR), Air Canada (YYZ)
1-Connection: BA, Lufthansa, Austrian, LOT, Iberia, Malev, Alitalia, Swiss, AF, KLM