Agree price is my main factor.
Especially School holidays Virgin know those with young kids and first timers will pay £££.
If you are buying 3 or 4 flights you can save £1000 indirect.
First time we flew indirect with DD she was 5 and it was fine. We are going indirect again in October.
Agree airline will help if you miss a connection - they held the plane in Philly for example as there were 70 connecting.
You also get the chance to volunteer to be 'bumped' off the flight. We did this several years ago and got a free overnight in chicago, business class the next day and I think $500 each towards a flight next year.
You also get a different type of passenger on indirect - older people, not many small kids, repeat travellers. It just makes things like check in/boarding easier and usually a quieter flight.
I personally like the break in flight - chance to pop to a real toilet, maybe grab something to eat and clear immigration. Arriving at MCO as a domestic flight was a breeze - straight off and into the hire car.