While what you're saying is correct, please note that:
1) Most of these flights only operate during the winter, when it's low season and it's easy to find low prices from TLV, too.
2) There are fewer airlines and destinations available from VDA compared to TLV, and the schedule is not as frequent.
3) All destinations available from VDA are in Europe.
Just to take a quick example: I searched for tickets from VDA and TLV with Ryanair to Milan (Ryanair serves both routes) in the third week of January. From VDA, you can find seats at 9.99 euros, while TLV is from 33.99 euros. While a 70% saving seems huge, we're only talking about 24 euros. For a family of four, that's 96 euros. If you're living in Beer Sheva, it's probably worth it to drive to VDA for the flight. But if you're living in Haifa, the cost of traveling to VDA is eating up your entire savings, plus the fact that you have to drive another four hours each way.
Also note that if you wanna take public transportation, you'll need to travel via Eilat both ways, thus making the trip to the airport extremely long and painful.