When using Thevenin's Theorem, why is R_thev of resistors calculated in parallel, when original circuit had them in series?
When calculating the Thevenin equivalent resistance, you're asking, if the current out the output port changes, how much will the voltage across it change. 

So you can think of it like a superposition problem with a hypothetical current source connected to the output port. When calculating the effect of this source, you need to zero out the other sources in the circuit. 

And when V1 is zero'd out (replaced with a short circuit) you'll see that R1 and R2 are connected in parallel.