I think, though everything that has been said certainly has merit, that there are two main reasons for people not liking ToD as much as Raiders (I'm not going to get into LC right now).
1) The mixture of dark stuff, over-the-top adventure, and slapstick comedy was too much for some people.
2) Folks wanted another Raiders, and came up short in that regard. Instead of a singing Egyptian, they got a Chinese kid. Instead of a tough dame, they got a shrieking damsel in distress. Instead of a slimy Frenchman, they got a cult leader. Instead of Nazis, they got something they've never even heard of. Instead of the Ark of the Covenent they got, once again, something they've never even heard of.