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Would it be cheaper to fly with them since they have very few passengers now-days?
Not necessarily.
Airline pricing is complex with many variables and sometimes counter intuitive. Pricing is both a science and an art and too many factors going into a particular airlines pricing algorithm to know definitively.
Factors like higher fuel usage due to longer distances and having to fly over more expensive airspace may drive prices up. See the Washington Post article which says
But now more Qatar Airways flights will incur Iran's relatively high fee, which may push the airline's ticket prices up, driving passengers away.