Google must work hard to convince its partner manufacturers that its new relationship with Motorola will not compromise its others.  Photo: Jon Snyder/Wired.com

Google’s always been happy to stay in the software business, which has suited gadget companies just fine. They’ve all benefited from Google’s willingness to license Android to anyone. But today’s announcement that the tech titan plans to acquire Motorola Mobility Holdings will make them wonder if Google is about to start playing favorites.

A lot of companies — HTC chief among them — have profited nicely with handsets running Google’s free Android operating system. But the news that Google is getting into the hardware business won’t win it any points among its hardware manufacturing partners, and it could provide an opening to competing platform owners like Microsoft.

“It’s difficult to be a Switzerland and provide software to these companies, while on the other hand go head-to-head with them,” John McCarthy, an analyst with Forrester, told Wired.com. “Google is taking a big risk here, and the company is going to have to work very, very hard to convince these other OEM’s [original equipment manufacturers] that the ground is level.”

Since 2008, Google has allowed manufacturers to license its Android mobile operating platform for their own devices. Companies like the fast-rising HTC have made boatloads of cash from Google’s foray into mobile. Sony Ericsson and LG, to name two others, similarly want to cash in on handset profits.

Typically, Google has used what Android chief Andy Rubin calls the “Nexus Program” model in dealing with hardware partners. Each year around Christmas, Google offers a gadget maker, a chip company and other product specialists early access to the latest iteration of Android. Everyone will “huddle together in one building, and around the holidays a new device pops out,” Rubin said in a conference call Monday morning. That process will continue, Rubin said.

“Moto will be a separate business and part of that bidding process,” he said.

In other words, don’t expect Motorola to get preferential treatment.

It’s a promise that Motorola Mobility’s hardware rivals are accepting at face value, at least publicly.

“We are supportive of Google’s acquisition of Motorola Mobility, as this is a positive development to the Android ecosystem, which we believe is beneficial to HTC’s promotion of Android phones,” HTC told Wired.com in a statement. “The partnership between HTC and Google remains strong and will not be affected by this acquisition.”

In a collection of quotes gathered by Google itself, Samsung, Sony Ericsson, LG and other companies used eerily similar language in praise of the acquisition, welcoming — as LG put it — Google’s “commitment to defending Android and its partners.”

But industry experts are skeptical that the partnerships will continue unharmed.

“It’s an incredibly awkward position for Google in terms of other manufacturers” said Gartner analyst Phillip Redman. “The complications of trying to run a hardware business are countless.”

“By entering into the hardware business, Google risks significantly weakening other OEMs’ commitment to the Android platform going forward,” Forrester analyst Charles Golvin wrote in a blog post today.

That could create an opportunity for other software companies, particularly HP — which will soon begin licensing its webOS software — and, of course, Microsoft and its Windows Phone 7 system.

“Product strategists at Samsung, LG and HTC are certain to revisit their Windows Phone hedge strategy,” Golvin wrote.

It is ironic that Motorola was the one Google chose for acquisition, given Motorola’s once-questionable commitment to Android. There were rumors that Motorola hired former Apple and Adobe engineers to develop an alternative web-based operating system, according to Information Week. Even Motorola software and services VP Christy Wyatt told Wired.com in February that Motorola wasn’t “religious” about its commitment to Android.

But the acquisition most likely was a play for Motorola’s trove of patents — somewhere in the neighborhood of 12,000 to 17,000 overall — that could protect Google from a multitude of future intellectual-property lawsuits, much like the Lodsys headache and Apple-Microsoft-Oracle lawsuit extravaganza that Google is navigating even now. Popular opinion suggests Google isn’t in it for the hardware.

At least, not primarily.