While Chrome's new policy is widely lauded, Google's dominance of the online ads business — in conjunction with the dominance of its Chrome browser and its influence on the group that selected which ads count as "intrusive" — raises some thorny questions.

The idea behind this move is pretty straightforward: If users don't have to deal with intrusive ad experiences, they may be less likely to download third-party ad blockers. Ad blockers crush revenue opportunities for websites that rely on ads to make money while also affecting the bottom line of ad providers like Google, which pays a fee to whitelist its ads in popular services like Adblock Plus.

Earlier this week, Google rolled out new filtering policies for its Chrome browser that will block all advertising on websites that serve particularly annoying ads, like autoplay videos with sound or full-page pop-ups.

Chrome has determined the 12 ad types which will trigger its blocking system based on standards set by the Coalition for Better Ads, an industry group where Google is a board member.

However, several members of the Coalition of Better Ads told The Wall Street Journal that they felt that Google had undue influence over the committees actions, because it spearheaded the research used to determine the intrusive ad types.

For example, YouTube's pre-roll video ads weren't included in research on intrusive ad types, which Johnny Ryan, the head of ecosystem at PageFair, a company that helps publishers protect against ad blocking, calls a "remarkable omission."

"Though Chrome's adblocker is a welcome improvement for users, it is not surprising that website owners are aghast that ads are being cleaned up on their sites, while Google's own formats go unharmed," he told CNBC.

Google told Wall Street Journal that it plans to test video ad formats in the future.

Meanwhile, some believe that the sheer scale of Google's business makes this move feel a bit like it's playing God with what users will or will not see online.

Google's global online ads business is bigger than its next five competitors combined, while Chrome has 59.23 percent browser market share across desktop and mobile, according to NetMarketshare.com.

"This gives Google even more power over the internet now than ever before," Rich Kahn, the CEO of digital advertising company eZanga tells CNBC. "When does one consider it to be too much power in the hands of one company?"

Even though users will be able to disable the adblock setting on Chrome, Kahn still sees the browser's move as dictating what websites can or cannot show and what internet users can or cannot see.

"I agree with the spirit of the CBA, there's no question we need to provide consumers with a better experience on the web," says Marc Guldimann, CEO of an ad startup called Parsec which had to phase out a version of it's product when Chrome first announced its changes.

"Unfortunately some of the implementation specifics, especially around research methodology, were less than ideal."