The other posters are correct...dropping off a car at a different location from where you picked it up is more expensive. Here are a few options in terms of the car situation:
- rent car at SD airport. Return car at SD airport. Use an airport transfer/limo/shuttle service to take your family from SD airport to DLH. Use a shuttle service from DLH to LAX at end of your stay.
- Rent car @ SD aiport. Drive to DLH. Deposit family & bags @ DLH. Return car at SNA John Wayne airport. Take taxi or Uber from SNA to DLH. Use a shuttle service from DLH to LAX at end of your stay.
- Rent car @ SD airport. Keep rental car throughout DLH days (keep in mind $20/day to park at the hotel). Return car at LAX. This is probably most expensive option.
I'm going to assume that you've already purchased your airline tickets, so switching to arrive & depart from LAX (instead of arrive at SD airport & depart from LAX) is probably not an option.
To figure out the cheapest option, you would need to price out all of the above 3 options. For example, I just looked on Budget Rental Car's website and put in a random pick up date in March from San Diego airport, dropping off 3 days later at John Wayne airport. It's showing a rate of $162 for an intermediate sized car. If you rent for 3 days and pick up and drop off at San Diego, the rate for that same sized vehicle is about $102.
Of course, this is without any special discount codes or anything that you might qualify for. Shuttle service from San Diego airport to DLH will probably run you more than $60, so if you're comparing just those 2 options, then it's cheaper to do a 1-way rental and drop off at SNA airport. Even when you add in the cost of a taxi from SNA to DLH, it's still cheaper than pickup and drop off at San Diego airport and then paying shuttle fees from San Diego to DLH.
Another option is way more complicated time wise and probably the most expensive option would be to do pickup/drop off at San Diego airport, then use public transportation to an Amtrak station, take Amtrak to Anaheim, then get on an ART bus to DLH...but ART doesn't drop off right in front of the DLH, so you'd have to hoof it with your bags or pay a taxi from the Anaheim Amtrak station to DLH. This will take the longest in terms of time.
Also, if this will be your one and only trip to Disneyland, then do a 5-day park hopper ticket if your budget allows. You'll be able to enjoy everything the parks have to offer without feeling rushed. You can do a lot in 3 days, but you kind of have to go commando style and it's really tiring after 2 days in commando mode (park open to park close).