Update: I've included some feedback from the comments. Thank you all.
Never forget that movies are to a certain degree illusions. In this case, it means the conclusions about the production you can draw just by watching the movie are limited. I haven't watched the movie in recent times but found enough resources online to explain certain aspects of the prodcution.
Yes, the movie is set inside a house, but all in all 4 filming locations were used, 3 for exterior scenes and the house was actually a set built in the studio. Each location shoot means people and equipment has to be transported, permits acquired, people hired to fence off the general public, and possibly extras need to be hired. In other words, it is expensive.
Building the set costs 6 million. They had a 3D model of the house which was useful to better plan camera positions and save a bit of money. Nevertheless that's a big chunk of the budget.
Nicole Kidman was originally casted but had to leave for medical reasons after the first 3 weeks of filming and was replaced by Jodie Foster. Consequently some scenes had to be re-shot. Also, Jodie got pregnant but a simple costume change (sweater instead of tank top) was enough to hide it, still any change costs a bit extra - although this is negligible.
When you watch a movie you often overlook some special effects and especially visual effects or CGI. These things costs a lot although they aren't that noticeable most of the time. Fincher is known for frequent use of visual effects and the long post-production phase is supporting this. CGI was more expensive to make back then.
Another big cost factor is filming with multiple cameras. They used two cameras, which also means two sets of very pricy lenses. And film stock. While one camera+lens bundle for high-end productions is around 500k-750k it is not clear how much it cost back then. However, not only cameras but all equipment costs are often shared amongst several productions over time, since most equipment is reusable, hence the impact on the budget might be smaller. Alternatively they could have rented the bundles for a couple of thousands per day. One important point is that filming with cameras from 2 angles complicated the lighting setup. You need more time to conceptualise, set up and tweak lighting when filming with two cameras simultaneously. More time on set means more saleries to pay.
Lastly, don't forget there are many more people working than the actors. Filming was done for half a year, followed by something about 9 months of postproduction. I haven't found dates for the pre-production phase. The saleries, including Foster's 12 million and 4 million for the script make essentially the majority of the budget.
All this taken together, a budget of 48 million is perfectly fine for this movie. Converting it to today's money is problematic since there are also drastic cost savers nowadays, like shooting digital instead of using film. So you cannot compare a movie made back then with a movie made today well.
There's a good documentary which helps you to get a better feeling of how much work such a production means: YouTube
What equipment they used: Shot on what
Some facts I mentioned were taken from IMDB and Wikipedia.