So basically for a month or so now the fans in the cabin have been having a strange issue were they blow air, then stop, then blow air, then stop and so on.

It doesn't do it every time but I would say 80% of the time it does.

It does it with the AC on or off & does it no matter what the fan speed is set at.

Is this a simple fix or something really broken?

Quick thoughts.

Have a look at the internet for the reset procedure, pushing and holding a couple of buttons at once often.

Do you have all the windows, doors, roof fully shut.

You could (carefully) clean out sensor vent(s), side of unit perhaps, and for mic and alarms while at it.

Have you checked for leaves and stuff at the air intake, change the cabin filter.

This time of year (warm, hot, too hot (for me anyway) the battery self discharges more, air-con is used more so another good time to check state of charge of the battery regardless of the headlights seeming bright enough and the engine starting easily (engine not starting is a last not first straw).

The battery state of charge probably has nothing to do with your issue but the computers can play up in all sorts of unexpected unrelated ways if the battery state of charge is just a bit too low for them, the stop/start not activating when it should and the computers cutting down on things like air-con to save battery power. Driving the car might charge the battery enough to put things off for a little while to return when the computer's threshold isn't reached. then the use of an appropriate battery charger maintainer following the instruction for charging in the car's 'Owner's Manual' and charger maintainer instructions. Charge as much as possible, slower and to full is best.

The reset procedure might sort it but if (also) the battery is in a lower state of charge than the computer likes use the battery charger maintainer.

HTH.

Let us know how you get on.

Sounds like you need to get the heater flaps recalibrated. There's a method to try if you have a search online.

https://www.google.com/search?q=skoda+rapid+heater+flap+reset&sca_esv=18be89dfcaae8ca6&sxsrf=AE3TifN1jJ2_rUJH64bvk2Xciu2ZRn4ZDg%3A1754995950877&ei=7hybaI2nNeOP7NYP2paEgQs&ved=0ahUKEwiN1u-xjYWPAxXjB9sEHVoLIbAQ4dUDCBA&oq=skoda+rapid+heater+flap+reset&gs_lp=Egxnd3Mtd2l6LXNlcnAiHXNrb2RhIHJhcGlkIGhlYXRlciBmbGFwIHJlc2V0SABQAFgAcAB4AJABAJgBAKABAKoBALgBDMgBAJgCAKACAJgDAJIHAKAHALIHALgHAMIHAMgHAA&sclient=gws-wiz-serp