Like many cheap MOS switches, the CD4066 has a relatively high on resistance. That's not the worst of it, because this resistance is very variable, with supply voltage, switch voltage, temperature, and specific IC. If you're trying to measure resistance, this variability shows up as a direct error in your measurement.
It's far better to use the MOS switch as a voltage multiplexer. This way, the variable resistance of the switch does not affect the reading significantly. Give each thermistor its own divider resistor. Buffer the output of the switch if the input to your ADC is very low impedance.
simulate this circuit – Schematic created using CircuitLab
If you really want to measure thermistor resistance through switches, then choose thermistors and switches that have at least 100:1 difference in their nominal values. You can get MOS switches with resistance down in single ohms. You can get thermistors with resistance in the 10s or 100s of kohms.