Here are some that I can conjure in my mind right now, it's from an article I read half a year ago, I think. Maybe longer than that, though it was quite interesting. Some of this is from that, some I just came up with off the top of my head.
Increased fuel consumption costs to make ETA in certain situations, either because the a/c itself is on a high utilization rate, or you need your passengers to make it for their connecting flights. ATC delays is also a major factor in increased fuel costs, which usually have a domino effect. Delays on the taxi will increase fuel consumption, and in certain extreme cases, may cause fuel related diversions, which is a separate can of worms altogether. Weather related delays have a similar effect. If an aircraft is late, and another aircraft has to be repositioned to take it's place, that can cost quite a bit of money.
Staff utilization rates will also increase, as staff and crew are likely to get overtime pay if their duty hours add up in the end. Then you have to consider aircraft that are leased on a per hour basis, or something similar. I'm not really familiar with these matters, so I can't tell you how that works.
Then there are the passengers, who's time is money, so to speak. The costs of compensating the passenger, if they miss their connection, can cost a lot of money. Putting them up in a hotel, for example, or direct compensation in terms of cash. Then the airlines actually put a value on passenger time, and that just blows my mind.