If the insole is *causing* pain, don't use it. You can hurt yourself if you try. (This is not a sign to panic, just be sensible and recognize that pain means something is wrong)

And no, not everyone has what you're describing. Matter of fact, because of the bone deformities in my feet, chances are my muscles just *can't* do what yours are doing. Your feet are different so your pain doesn't necessarily mean what my pain does (and trust me, if you had the disorder that gave me my misshapen bones, chances are a doctor would've found it already. usually it makes your feet visibly the wrong shape).

Are you making sure to keep the ball of your foot on the pedal? I keep my feet in place without the usual toe clips or clipless assists because if I don't... my feet hurt. Nice little immediate feedback loop. A lot of people don't keep the ball of their foot in the right place as easily tho, and toe clips or clipless pedals are meant to help them maintain the right form.

Have you tried taking breaks before your feet start to hurt? Have you tried using gentle stretches and massage to reduce the pain? What happens if you only use the insole on the left, and let your right foot support itself?