The tough regulations for net neutrality are a wild card when it comes to the $45 billion merger of the nation’s two biggest cable companies, industry observers say.

On the one hand, some analysts argue that the new Federal Communications Commission (FCC) regulations will eliminate many of the harms that might come from combining Comcast and Time Warner Cable, giving regulators reason to approve the deal.

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But if the new rules are a symptom of a larger trend at the FCC of cracking down on big companies, it could spell trouble going forward.

“I think we’ve seen an FCC that has been much firmer with the broadband industry than a lot of people expected a year ago,” John Bergmayer, a senior staff attorney at Public Knowledge and an opponent of the merger, told reporters on Monday.

“It shows that you have an FCC and a chairman at the FCC who is really not afraid to take on established industry [and] do what he thinks is right.”

In recent weeks, as the regulatory review of the merger has stretched on at both the FCC and the Justice Department, some analysts have begun to downgrade their expectations that the deal will be approved.

They have pointed to not just the net neutrality rules, which treat broadband Internet like a public utility, but also recent moves to block state laws limiting towns from expanding their own government-run Web services and the FCC's decision to increase the internal benchmark for what qualifies as high-speed broadband.

On Thursday, a day before the agency voted to issue the new Web rules, it sent letters to a handful of programming companies inquiring as to whether or not Comcast or Time Warner Cable had tried to limit them from distributing TV shows and movies online, in a sign that officials aren’t taking their foot off the gas.

“If the FCC had decided that net neutrality solves the merger, it sure doesn’t seem like it at the FCC,” said Jeff Blum, senior vice president at Dish Network, which is also opposed to the merger. “They’re conducting a very serious review and looking at areas that net neutrality doesn’t cover.”

Critics say that combining the two cable giants would give Comcast unprecedented power to dictate how other companies sell or transmit their programming, which the companies deny.

Company officials have repeatedly pointed out that Comcast and Time Warner Cable don’t compete in any of the same markets, so the merger won’t cause any customers to lose an option for service. They have also promised to spin off about 2.5 million subscribers and take other steps to mitigate potential harms.

Comcast chief financial officer Michael Angelakis said during an earnings call last week that he was still “optimistic” that the merger will be approved in the next few months. Company executives also appeared to dismiss the notion that they would refrain from joining any lawsuits against the rules, which are looming in coming months.

Still, the mere fact that the rules have been issued may give corporate executives some reason to breathe easy.

"If your fear of a larger, bigger, badder Comcast is that we can't regulate them, now we have regulation,” Daniel Ernst, an industry analyst at Hudson Square Research, said on CNBC’s “Squawk Box” on Friday.

“So there's no legal reason to withhold the merger."

— Updated at 2:37 p.m.