This is very specific to LY.
Just do the math: They have night flights to LAX, JFK, EWR, MIA, BOS, PEK, BKK, HKG, many of which are on massive 747's and 777's. All their flights use the same 8-16 check in desks (don't remember exactly) and they tend to have large families that travel with lots of bags, strollers, car seats, etc'
Meanwhile Delta or United have one flight on a smaller plane and they use 3-4 check in desks. The LY line is 40 minutes on a good day and 2:00 hours on a bad one.
If I ever flew LY in economy with my family, I would probably spring for the $140 or so that the VIP service cost.
Wouldn't you pay $140 when the alternative is suffering like crazy with the whole family for two hours? If you are that cheap, take the bus to the airport instead of a taxi or better yet, don't fly ELAL.