I didn't play these, but I played plenty of other games from that era with really clunky controls. Mega Man Legends was a favorite of mine and that had wonky controls.
In those days, 3D was still new and exciting, and there weren't that many games that did it well. Tomb Raider was in development at the same time as things like Mario 64, so it's not like they could really see what worked and what didn't. So, if we wanted to play exciting new games, we worked through the quirks. Especially since they weren't really making a ton of 2D games anyways.
Nowadays, if something has bad controls, or even just a novel control scheme, there are more options than you'll be able to play in a life time. Unless there's some particular reason you really want to play the original Tomb Raider games, you may be better off just playing something else.