Soreness after flights, and rudders

Does flying leave you sore if you haven't flown in a while or if you
are new to flying? I'm thinking of muscle fatigue from being in an
unusual position for long periods, and in particular I'm wondering if
keeping one's feet on rudder pedals for hours at a time leads to any
soreness afterwards. Or do you even keep your feet on the pedals all
the time? Since apparently most autopilots don't use the rudder, even
running on autopilot might not eliminate the need to have feet on the
rudder (?). And if pushing the pedals forward applies the brakes,
does this mean that you have to hold your foot back whenever it's
resting on the pedal? Does it hurt anything to apply the brakes in
flight?

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