JSON is used as a query language because it's fast, easy to parse and easy to generate dynamically. If you have a query interface for users, SQL is probably a better choice, but Mongo chose JSON for performance reasons.

If you don't like dealing with it directly, use something like MongoEngine so you're not working with the raw queries, or if having readable, easy to understand queries is important, use a SQL database.

Everything is a compromise, with Mongo's query language you're sacrificing readability for performance.

( This is not a comparison of a SQL database to Mongo, just the time it takes for a SQL engine to parse the query into an execution plan )