Installed Harbor Breeze ceiling fan/light with remote unit - wall switch no longer functions
Taking the information you have given us, what you are describing doesn't make sense. The only way you could connect the fan without it operating on the switch is to bypass the switch, if it is a mechanical switch (not a controller from the previous fan). Meaning you have somehow tapped the line side to the switch and disconnected the switch leg returning to the fan. 

You need to take a voltage tester and check which wire is the switch leg and which wire is the line side hot to the switch by turning the switch on and off and seeing which one is permanently hot and which one is the switch leg and reconnect them to reinstall a mechanical switch. 

If the switch was a controller installed for the previous fan, you need to replace it with a standard mechanical switch.

Happy new year and good luck.