A flight into a secondary airport can save eighty dollars on the ticket and cost more than that in transfers. The bus or train into the city, the extra hour at each end, and sometimes a night near the airport all belong in the same comparison. Fare alone rarely decides which option is cheaper once you land at eleven at night.
Price the transfer before you book
Look up the airport transfer in advance and note the cost per person and the journey time. A city-centre airport with a ten-dollar train beats a distant one with a forty-dollar taxi every time, even when the distant fare is lower. Multiply by the size of your group, because transfers scale while fares do not.
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Late arrivals add a second cost that is easy to miss. Services stop running, so a taxi becomes the only option, and the price at that hour is higher than the daytime rate. If the arrival is after ten in the evening, assume the most expensive transfer method and redo the comparison on that basis.
A connecting flight and a direct flight trade differently
Compare a direct flight against one connection on total journey time, not on ticket price. A connection adds two to four hours and, on separate tickets, all the risk of a missed onward flight. On the same ticket the airline rebooks you; on separate tickets you buy a new seat. That distinction is worth paying for on the last leg home.
Actionable step: build a simple sheet with fare, transfer cost, transfer time and arrival hour for each option, then sort by total. Three minutes of arithmetic usually reorganises the shortlist completely, and the cheapest fare often lands in the middle once transfers and luggage are counted.
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Baggage fees reset the ranking

Low-cost carriers price the seat low and the suitcase separately, so a family of four with checked bags can pay more than on a full-service airline. Add the baggage fee, the seat selection and any card surcharge to the headline fare before comparing. The advertised price is the beginning of the calculation, never the end.
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