The writers probably simply thought "Emmerdale is meant to be in Yorkshire. Does anyone know of any airports in the county?". They then never bothered to check which flights operate from the one which somebody suggested. Accuracy in detail in TV soaps is often missing!
Alternatively, if they wanted to film at the airport, Leeds/Bradford might have refused them permission(or simply wanted too much money).
People living in the Yorkshire dales, who wanted to get to Prague, would indeed probably be most like to fly with easyJet or Jet2 from Leeds/Bradford. If there were no convenient flights from there ,they might also consider using Jet2's services from Newcastle, Manchester or East Midlands.
If it's accuracy you want though, I'll point out that Doncaster/Sheffield Airport ceased using the name 'Robin Hood' at the end of last year ;-)