I'd guess there are many factors. For instance, in manufacturing, small differences in raw material cost and process requirements can have a big impact.
However, in this case, I'd say it comes down to temperature resistance: polyester (PET or PETE) does not do well at high temperatures, PP does. A reusable cup for microwave use is going to have hot (probably boiling) liquid in it.
From Plastic bottle - Wikipedia:
Polyethylene Terephthalate (PET, PETE or polyester) is commonly used for carbonated beverage, water bottles and many food products. ... This material does not provide resistance to very high temperature applications—max. temp. 200 °F (93 °C).
Polypropylene (PP) is used primarily for jars and closures and provides a rigid package with excellent moisture barrier. One major advantage of polypropylene is its stability at high temperatures, up to 220 °F (104 °C). Polypropylene is autoclavable and offers the potential for steam sterilization. The compatibility of PP with high filling temperatures is responsible for its use with hot fill products. PP has excellent chemical resistance, but provides poor impact resistance in cold temperatures.
Here's an additional source: The 7 Most Common Plastics and How They are Typically Used. In summary: PETE is easily recyclable but breaks down under both heat and light exposure. So it gets used for one-time-use applications but isn't suitable for reusable containers.