Originally Posted by JJeffrey

Different airlines have different flexibility when it comes to schedule changes. Since you booked through IB it's up to the IB policy/agents to move you to something better. They could easily change your flight for no cost but they're choosing not to since your new flight times are still technically legal.

IB is well known for having pretty horrible customer service so this rigidity isn't really surprising unfortunately. If you had booked through AA then it would be relatively easy to call and get moved to a more comfortable connection.

As everyone has noted if you depart SAN on time or even slightly delayed then you'll make it. If you're sitting at SAN and the flight to CLT gets delayed by more than about 20 mins then speak to an agent and get rebooked right then from SAN, do not wait until you get to CLT to sort it out.