How the smaller terminals differ from Mexico City and Cancún
Mexico's big gateways, Benito Juárez in Mexico City and Cancún International, handle long-haul traffic and run at full speed year-round. Regional airports work on a different scale. A place like Oaxaca's Xoxocotlán or Tuxtla Gutiérrez's Ángel Albino Corzo has a handful of gates, one or two cafés and a single baggage belt, so you clear security in minutes rather than an hour. That convenience is real, but it comes with fewer backup flights: when a morning departure is cancelled there may be nothing else until the next day, and the airline counter is the only place to sort it out.
Check-in habits matter more here. Many regional carriers close counters 45 minutes before departure, tighter than at the big hubs, and online check-in is not always available for smaller operators. Arrive two hours early even though the terminal looks empty, keep a printed or saved copy of your booking, and confirm the baggage allowance at the time you book rather than at the gate, since regional fares often price a checked bag separately. If you are connecting to an international flight the same day, leave a generous buffer; a morning domestic hop can eat an afternoon if weather or aircraft rotation goes wrong.
Which cities are worth flying into and which to reach by road
Flying makes the most sense where the road is long or winding. Oaxaca to Puerto Escondido is roughly seven hours by road through the Sierra Madre del Sur, while the flight takes under an hour, so for a beach add-on it is worth the fare. Tuxtla Gutiérrez to San Cristóbal de las Casas is a two-hour drive on a good road, which is manageable, while flying into Tuxtla from Mexico City saves a fourteen-hour overland haul. Mérida and Villahermosa are both well served and make sensible bases for Yucatán and Chiapas loops respectively.
Some short hops are not worth the hassle. Mexico City to Puebla is about two hours by bus from the TAPO terminal, and by the time you reach the airport, check in and land, the coach has already arrived. Similarly, Querétaro to San Miguel de Allende is a little over an hour by road; skip the flight. For the Yucatán, flying into Mérida and out of Cancún (or the reverse) avoids backtracking, and both airports have frequent regional service. I would book that open-jaw pattern over a return to the same city every time, especially for a two-week trip.
Timing, seasons and the practical bits
The dry months from November to April are the steadiest for regional flying, with fewer afternoon storms than the May-to-October rainy season, when delays stack up in the late afternoon. If you must fly in summer, take morning departures; the weather usually builds after midday. Fares on regional routes vary widely by season and how far ahead you book, so compare dates rather than assuming a fixed price. Small airports often have limited ground transport, so check whether your arrival time still has combis, taxis or ride-hailing coverage, and arrange a transfer in advance if you land after dark.
Baggage is the other recurring friction. Regional aircraft have smaller overhead bins, so a roll-aboard that fits a mainline jet may be gate-checked. Pack a small personal item with essentials, keep medication and documents with you, and photograph your bag before handing it over. At the airport, buy water and snacks after security if the terminal offers it; some regional cafés close between flights. Finally, keep your hotel booking flexible. With 198 hotel views but only 3 checkouts across the site in the past week, it pays to reserve a room with free cancellation in Oaxaca, Mérida or San Cristóbal, so a flight change does not cost you a night.
Where I would stay on a regional route
For an Oaxaca and coast trip, I would book two or three nights in Oaxaca's centro histórico, within walking distance of the zócalo and Santo Domingo, then fly to Puerto Escondido and stay near Playa Zicatela or Carrizalillo depending on whether you want surf or calmer water. In Mérida, the centro around Paseo de Montejo and Parque Santa Lucía puts you close to restaurants and the ADO bus station for day trips to Uxayal or the cenotes. San Cristóbal rewards a stay in the grid north of the main plaza, where the altitude is gentler and the streets quieter at night.
Book the hotel before the flight on regional routes, not after: accommodation in these cities fills for festivals and long weekends, and a refundable room gives you room to move if a schedule shifts. Use the search filters for free cancellation and breakfast, and check the distance from the airport or bus station rather than trusting a map pin. For a first trip, I would pick Oaxaca as the base and add the coast, keeping Mérida for a separate Yucatán itinerary rather than trying to combine both in one week. It is the pattern that leaves the least time in transit and the most in the places you came to see.