You don't have to have spandex for the legs, for me synthetic hiking pants have done fine, and also courds in the winter. The problem was basically two things- jeans were abrasive, wearing away hair follicles, and they didn't breathe, trapping a lot of sweat/humidity.
If you're riding for very long, though, you will probably want padded shorts. I used to think they were silly, but after a couple of rides where my butt was seriously sore afterwards and one where my junk went numb, I swapped out my old saddle for one with a split down the middle and started wearing padded shorts and now I can bike for 40+ miles without getting sore.
I like my cycling tunic/jersey thing because it gets really good airflow, but I've gone on long rides in just a plain old t-shirt, too.
IMHO a lot of this is the need for adaptation to increased stress.
I've heard a lot of stories of people going through quite a few different saddles until they finally find one that "works", but in the meantime they've also been spending a lot of time riding and have toughened up their posterior. So was it the saddle or the adaptation that solved the issue?
I'll wear padded shorts and lycra for a looong ride (2-6 hours) as it's just more comfortable, but plain tights under short and a cotton tshirt is fine for the 30min commute.
