The argument can be made that the reason El Al is more expensive is because they don’t fly on Shabbos. Spending the extra money on El Al might help them to retain their shomer shabbos status. If they don’t make enough money, they may consider lowering their prices and start flying on Shabbos to make up the lost revenue.
Additionally, supporting Jews is always better than supporting non-Jews (though $500 may be too steep a price for this).