The vast majority of Minecraft servers earn money through selling in-game ranks/items, but this isn't the only option. This tip covers this option and a few alternatives!
Methods to monetise a Minecraft server:
Selling in-game ranks/items is an approach used by the vast majority of Minecraft servers, as it can easily be configured using a plugin such as Buycraft - which allows you to set up a web store hosted by Buycraft where players can buy in-game ranks/items. The benefit over creating your own system is that Buycraft deals with payment processing related issues, so this can be done with very little technical expertise. For new servers using Buycraft is free, as you grow they begin charging you based on how many donations you receive/which perks you want. Pricing information is available here. Ensure that any perks you provide follow the Mojang EULA, a list of EULA-compliant donator perks/commands can be seen here.
Displaying ads in-game is an alternative way to monetise your server. The plugin CommandAd provides two ways to do this. The first option is for your users to click a link to view an ad on a website in exchange for a reward, and the second for the user to view an in-game ad displayed on maps using an extension plugin called AdMaps (unsure if this option complies with the EULA, but you can contact the plugin developer to confirm this). Both options give you around $5 per 1000 views, which if you're getting a few hundred players per day can add up!
Patreon is something few Minecraft servers take advantage of. Popular among YouTubers, it allows any content creator to create a Patreon page where followers can become a 'patreon' and donate money to the creator per month in exchange for a reward of some sort or just to support the creator. Many people who donate to Minecraft servers do so to support the server rather than gain in-game perks, so although this won't bring in as much as a donator rank - it will bring in a small amount monthly that can help pay your server bills.
Merchandise is a more creative option to monetise your server. By selling things like shirts, posters, mouse mats - any item your players would like - branded with server artwork, you can earn some money each time a player buys an item of merchandise. By using a service such as Spreadshirt, where you can upload artwork and display a store page for your users, you can get a commission of $10+ per item sold with your artwork on it! If you sold say 10 items per month this way you can earn a decent amount of money! You can even try making and shipping the shirts yourself if you're feeling creative, although this often has lots of hidden costs!
Simo389 has been running Minecraft servers since 2012, and developing for them since 2013. Currently he runs MineRifts, a YouTube channel and shares advice in these tips on how to publicise & improve your own Minecraft server.