Yes, for a non-profit 50 million $ just laying around seems like a lot. The WMF page says there are 230 employees for a revenue of 38 million $ (mostly from donations). You can hardly claim they are being secret about it. Also, paying 230 ppl an avg of 50,000$ a year is already 11 million$ ( so it's not a trivial amount, and if the avg is higher that goes up by a margin as well).
However, when you look at the presence of WikiPedia on the internet, it's basically first hit on google in every search on every possible subject. It's probably the number one source for people to find information about a subject. They have a HUGE presence. If someone had to put a value on that, it would be worth billions. Look at other internet companies. Google (365 billion $), facebook (200 billion $), etc... Sure, they are not Google or Facebook, but would definitely be valued in the billions. The 50 million $ is just change compared to their net worth.