I think it's difficult to differentiate between "pain" and "discomfort" when exercising. It's like asking someone with a tattoo if it hurt. Some people don't mind getting them at all, others pass out as soon as the tattoo gun hits their skin.
I'm 65, and getting back into cycling after a long layoff. I've been gradually increasing my mileage and working on strengthening my leg muscles again. At the end of a ride, I may feel some discomfort - the kind of discomfort you may feel after working muscles that haven't worked that hard in awhile. It's nowhere near debilitating, nothing a good hot shower and a little rest won't take care of. I figure if I'm not a little sore, I haven't exercised hard enough.
Pain is another issue. I have an old knee injury that to this day will rear it's ugly head on occasion. If I'm out on a ride (or a walk, climbing stairs, or any other type of exercise) and I feel that *stab* in my knee, I stop - right away - and evaluate my feeling. Sometimes it just means I have to ease up quite a bit to get to where I was going, sometimes it means I grab my cell phone and call my wife to come pick me up in the car.
Sometimes something that causes discomfort (bike fit, cleat position) can lead to pain if ignored long enough. That issue can be addressed in various ways. Pain/discomfort due to injury or (let's face it) age can sometimes be helped (if a recumbent alleviates your neck or back pain and allows you to ride, I have zero issues with them) but sometimes it's just a matter of knowing your limits (distance, speed, time on the bike) and staying within them.