Big blockbusters aside, very few films make their money back on theatrical release. Think of theatrical as more of a way to advertise rather than profit.
Studios won't risk anything that they don't see as a lock with either a big name star, director, of something with a previous existing fan base such as Transformers, Terminator, Man Of Steel, blah blah. Its even gotten to the stage where potential scripts (after getting through the slush pit) are then sent through a machine that then compares the script with a shitload of statistical data on movies that have been commercially successful previously to recommend changes. It costs 20k a pop to do it, but for a big blockbuster that's chump change.
Long story short, don't expect anything fresh and new to come out of the big studios. The ironic thing is this process would actually reject Batman if someone were to only think it up now. lol.
As for how they make their money, it's not easy, but there are local sales, foreign sales (there are hundreds of countries/territories to sell through), theatrical, TV, digital, on demand etc that can all bring in a fee for the film. These are things that can continue to drip money in for years.
The other thing is transmedia. Think about things like the Dead Space game that also had a DVD released with it to buy. Toy lines, apps, merchandise in general etc. Then there's the 3-4 different versions of the film that will eventually get released over time.
The fact is, DVD is going to die out and some point, even physical sales of films in any format will fall. That's why outside of the big blockbuster movies, movie budgets are actually falling quite substantially. 3mil is the new 10mil by today's standard because outside the big blockbuster nobody can create or justify the value of projects and are forced to bring their budgets down. This may not actually be a bad thing, but the big blockbusters which get all the press make it look like budgets are getting bigger.
Also I think for a commercial success you need your budget and then 50% of that budget for marketing. So a 100mil film requires an additional 50mil to give it a genuine shot of making it's money back. I may be wrong on that, but I'm pretty sure it was 50%.