MongoDB uses BSON (Binary encoding of JSON) format for storing documents in collections. And as you know Node.js is JavaScript runtime. As @kayandrae said, Node developers usually relate more to BSON format rather than traditional relational DB. Storing JavaScript objects in terms of documents (in collections) just makes sense to them. MongoDB is schema-less and therefore far more relaxed than SQL DBs. So, if a Node.js developer needs to store one more property in a document they will just add one (just like you add a property to a JS object) and save the document.
Finally, JSON format is native to JavaScript and since MongoDB lets you store JSON documents Node + MongoDB makes sense.