Seaport Airlines has reduced its service between San Diego and San Felipe to three days/week. You can now fly Thursday, Saturday or Sunday. The schedule is shown below. It is also important to note that the commuter terminal at San Diego International (SAN) has closed down effective 4th.June so the Seaport flights will depart instead from Terminal 1, Gate 11 (next to Frontier Airlines).
The current round-trip fare between San Diego and San Felipe is $289.78 and an additional fee of $25 (cash only) may be required to purchase a tourist card on arrival in San Felipe if you do not hold a Mexican immigrant visa. To book a flight, it is best to call the airline’s toll free number 1 888-573-2767 as the booking engine on their website is an exercise in frustration to use (it cannot tell you what dates flights have seats available).