I would say this from my personal experience.
Asking Fees for Featured Ads
Even if you allow users to submit advertisements for free, you can offer them to make their ads featured. This typically means, their ads will be highlighted somehow or appear at the top of the categories, search results or on the homepage within a slider. This function is integrated into almost all of the premium templates and plugins.

featured-ads-section

Create Membership Packages
Some scripts and themes support various membership packages. This means you can set up a specific time, usually a month, while the members can submit ads. You can set the maximum number of ads or you can let them submit as many as they want.

Another option can be if you sell advertisement packages which means you can allow them to submit a particular number of ads for the price. For example, you set up 10, 20, 30 submission packages which they can use until they use up all the submissions.

These are perhaps the best solutions since they may subscribe for a longer time which means regular income for you.

wordpress-classified-theme-membership-packages

Ask Fees for Ads Submission
This is the simplest way to make money. You can make your entire website paid or just some categories and you ask a fee for each of the submissions.

Selling Banner Ads
If you have a niche classified website with a lot of traffic, you can sell ad spaces as well. There are marketplaces you can use to find advertisers.

Monetize Unused Spaces via PPC Ads
If you need an even simpler solution to make money with the unused areas of your website, you can place PPC ads such as Google Adsense. If you have a good amount of traffic, they can earn you some extra bucks daily.

Promote Affiliate Products
Since you are the owner of the ads listing website, you can promote affiliate products. Submit ads with your referral links with detailed descriptions. I do not recommend enabling this option for the other users since you may have a lot of spam.

Build an Authority Site and Sell
If you pick the right niche, your website has a lot of visitors and it is an authority in its field, you can sell it as well. There are a few marketplaces where you can sell your classified website, the most well-known one is definitely Flippa.com.

As you can see classified ads website monetization is really simple, the harder task is to get tons of targeted traffic..

For more queries you can consult me.