I haven't flown their intra-California flights, but I've flown with them in some other small markets.

SeaPort currently flies single engine Cessna 208 Caravans, these planes only seat 9 passengers.

I'm not sure which route you're looking at, but most of their through flights are just stopovers to pick up or discharge passengers. If you fly Sacramento - Visalia - Burbank, you probably won't even have to get off the plane in Visalia (and if you do, you'll just be stretching your legs alongside the pilot).

If SeaPort is selling the flight as a valid connection, I wouldn't worry about it.