Will you see ads on this device in the future? (David Paul Morris/Bloomberg)

For the last two days, Marco Arment has been the envy of the Apple iTunes store. His $3 app, "Peace," which allowed users to block all ads when they surf the Web on their iPhones, held the title of most downloaded paid app.

But on Friday, Arment took the program down -- citing concerns that it was hurting companies who rely on ads to stay in business and "don't deserve the hit."

Arment's app and other ad blockers have skyrocketed in popularity since Apple added support for the technology in its newest mobile operating system, iOS 9, which launched on Wednesday. But the programs also are at the center of an acrimonious debate over the economy and future shape of the Internet. A huge swath of companies, from giants such as Google and Facebook to start-ups and media organizations, offer their services for free -- if users tacitly agree to view targeted ads based on their online habits.

Arment appeared to acknowledge that the backlash over his program prompted him to pull it from the iTunes store.

"It’s simply not worth it," he wrote in a blog post. "I’m incredibly fortunate to be able to turn away an opportunity like this, and I don’t begrudge anyone else who wants to try it. I’m just not built for this business."

Online advertising is part of the fundamental trade-off that powers much of the web: Almost everything users do online is tracked by advertisers who fund the "free" services consumers have come to expect -- e-mail, social networks, and access to online news.

Google and Facebook have built online empires based on this idea. And a whole slew of other companies have sprung up, serving as middleman between publishers and advertisers who create detailed profiles of users as they travel across the Web, measuring the efficiency of ads, and setting up what amount to real-time auctions for digital ad space.

"Each of these intermediaries takes a cut, fragmenting the revenue that used to go more directly to publishers," said Jonathan Mayer, a computer scientist and lawyer who researches the online advertising industry.

Critics say the resulting system can be irritating, invasive and sometimes downright unsafe for users.

Ads slow down loading time, especially on mobile devices. And they can take over whole screens, putting a layer of frustration between users and the content they actually want to read on the Internet. Privacy advocates worry that consumers may not understand just how intimately they are being tracked or have a say over what happens with that information in the long-term. And a wave of "malvertising" attacks have used legitimate advertising exchanges to deliver malware to people visiting even some of the most trusted Web sites.

Ad blockers can mitigate these problems, but they also turn users into freeloaders -- getting goods without "paying" for them with their attention, personal data and, ultimately, ad clicks.

When he first launched Peace, Arment argued that the online advertising system had gone so far that consumers could be justified for opting out:

The “implied contract” theory that we’ve agreed to view ads in exchange for free content is void because we can’t review the terms first — as soon as we follow a link, our browsers load, execute, transfer, and track everything embedded by the publisher. Our data, battery life, time, and privacy are taken by a blank check with no recourse. It’s like ordering from a restaurant menu with no prices, then being forced to pay whatever the restaurant demands at the end of the meal.

If publishers want to offer free content funded by advertising, the burden is on them to choose ad content and methods that their readers will tolerate and respond to.

Yet publishers are now more than ever at the mercy of the online advertising industry. Traditional outlets have been seeing their revenues from print products plummet. They and newer media companies have been scrambling to grab a piece of the online advertising pie, even though it pays out far less than print ads.

The problem is growing worse as digital advertising becomes increasingly commodified, paying publishers less on each ad and incentivizing them to compensate by generating more clicks. It’s a downward spiral that publishers ignore at their peril, according to media critic and New York University journalism professor Jeff Jarvis. The media industry can either watch its business model crash, he argues, or reverse the trend by serving only high-quality ads that restore trust in the publisher. Some outlets operating on this logic have already begun turning away certain types of advertisers.

“Nobody's argued with the people at the ad agencies and marketers and brands. We have a small window here before it's too late,” said Jarvis. “You have to be willing to fire advertisers."

Some news organizations have also made appeals directly to consumers. The Washington Post recently experimented with ways to discourage the use of blockers, redirecting some online readers who have installed the program to a page urging them to subscribe. The test ended this week, according to Kris Coratti, The Washington Post's vice president of communications.

Ad blockers have been around for a long time, but their popularity has grown as ads have become more pervasive and as users have learned more about the tracking methods behind them. Some 45 million people in the U.S. are actively using ad-blocking software according to one study published by Adobe and software company PageFair last month -- a figure that increased 48 percent between June 2014 and June 2015.

And as consumers shift more of their Internet browsing from desktop to mobile devices, Web site operators fear that iOS support for ad blocking will lead to further declines in revenue. Apple’s Safari browser accounts for over half of the country’s mobile Web traffic, according to the analytics firm StatCounter.

The programs have become so pervasive that some major advertising networks, such those run by Google and Amazon, have paid ad blockers to ensure their content makes it through the filters, several news organizations have reported.

It's in this complicated landscape that Arment and others launched their ad blockers.

"Ad blockers come with an important asterisk: while they do benefit a ton of people in major ways, they also hurt some, including many who don’t deserve the hit," Arment wrote in a blog post about his decision to remove the app. Still, he added that he thought ad blockers were necessary programs and recommended several competitors.

Indeed, as soon as Peace came off the iTunes store, another ad blocker called "Crystal" took its place at the top of the charts.

Dean Murphy, the developer, made his intentions clear: "I have no plans to remove Crystal from the store."