On the surface, USAA looks like a prime example of how Apple is making new inroads into large enterprises. The financial services company has deployed more than 500 iPhones and 300 iPads, has about 200 Macintosh computers, and it’s considering bringing in more Macs to displace some of its Windows desktops.

San Antonio-based USAA has also released a customer-facing app for iPhones and iPads, and it’s considering developing others for internal use. “There seems to be a simmering demand for them, and some good business cases,” says Mike Pansini, assistant vice president of IT infrastructure architecture at USAA.

But as is the case at many large companies, USAA’s relationship with Apple is more measured than it might first appear.

The iPhones and iPads have been limited to the executive management group — USAA has no plans at present to expand their use more broadly — and its 200 Mac desktops and laptops, mostly used by developers, represent a small fraction of USAA’s inventory of personal computers. The rest of its information workers — some 23,000 people — remain solidly on the Windows platform.

It’s certainly true that Apple is making inroads into large enterprises. In a recent Computerworld survey of 367 IT managers, 73% of the respondents said they’re providing or supporting Apple products in some way. But 25% still aren’t supporting even one iPhone, Mac or iPad (and 2% didn’t know if they were). The 143 largest enterprises in the survey — those with more than 1,000 employees — had the same ratio: 73% support an Apple product; 27% don’t.

Although many enterprise IT organizations are accommodating user-owned or company-issued iPads and iPhones, they’re providing carefully controlled access to a limited set of corporate IT resources, such as the Internet and corporate e-mail.

Apple is also making headway with corporate desktops and laptops: 55% of the survey respondents support at least one Mac, and 60% support MacBooks. But in most of those cases, the IT shops are supporting 100 or fewer Apple machines. And the Mac’s penetration into large businesses is miniscule when compared with the number of Windows-based machines ordered each year.

Furthermore, IT managers say Apple isn’t always supportive of their needs, and the Computerworld survey shows that many of the obstacles Macs have always faced in large organizations still exist, including the following:

• Mac versions of enterprise applications either don’t exist or lag behind releases for Windows.

• There are few tools for managing Macs on a large scale and integrating them into a Windows-centric enterprise.

• The perception remains that Apple products are expensive.

• IT managers say that service and support options aren’t up to enterprise standards.

• Apple doesn’t provide a product road map to help IT managers make plans.

• Enterprises have limited opportunities to negotiate prices for Apple products.

At the same time, the survey and interviews with enterprise IT executives indicate that Apple’s position has improved in some areas:

• More businesses are buying or building platform-agnostic applications that can accommodate Apple products.

• Enterprise-class management tools for Apple products continue to evolve.

• Apple’s prices are becoming more competitive.

• The trend toward Web-based enterprise applications has made integrating Apple products easier.

• In the tablet market, competitors arguably have yet to offer a product that’s a better value than the iPad.

Apple still doesn’t play in the low end of the desktop and laptop markets, but it’s much more competitive than it once was on the types of units enterprises tend to buy, says Laura DiDio, an analyst at market research firm Information Technology Intelligence Consulting (ITIC). Mac products, which once sold for a 30% premium over comparable PCs, have come down to earth. “Apple doesn’t get a lot of credit for that,” she says.

But IT executives tend to see Apple as a provider of consumer-oriented devices, not a full-on enterprise partner. “In the Windows space, we’ve got a full-time Microsoft support team that is very engaged in what we do. With Apple, they haven’t matured into that yet,” says USAA’s Pansini.

On the desktop side of the business, an iPhone/iPad “halo effect” may have been partially responsible for a 255% increase in Mac desktop and MacBook sales to enterprises in 2010, as reported by IDC. But that figure is somewhat misleading. Shipments of Mac products to large businesses still represent less than 2% of the overall enterprise PC market in the U.S., according to IDC figures. “Apple’s market share is absolutely insignificant,” says IDC analyst David Daoud.

Nonetheless, Mac sales to the enterprise are up sharply, relatively speaking. More than a quarter (27%) of the Computerworld survey’s enterprise IT respondents who support Apple products said support for iOS devices had either sparked interest in adopting Macs or had resulted in greater adoption of Macs. “I wouldn’t say they’re buying Macs in droves,” says Gartner analyst Michael Silver. “But more Macs are being supported as part of bring-your-own-computer initiatives.”

However, when it comes to media tablets, Apple’s iPad owns the category, accounting for more than 90% of the 300,000 units shipped in the U.S. for commercial use in 2010. Increasingly, users are picking their own smartphones and tablets and are asking to use them for work. IDC expects the number of commercial shipments of media tablets to jump to 1.3 million this year. “It’s become an unstoppable force,” says Silver. “It’s gotten harder to say no.”

While most large organizations aren’t supporting large-scale deployments of Apple products, Genentech is an exception. The IT department at the South San Francisco-based biotech company supports more than 2,500 Macintosh computers — about half of the desktop population — and some 8,000 iPhones. And it has made the most of user interest in iPads and iPhones, developing apps for tasks ranging from CRM to purchase order approvals and expense reporting.

That’s driven in part by the fact that Genentech allows users to choose their own desktop computers. Even so, Macs tend to be used in groups that are less dependent on Windows applications, such as sales, marketing and research. “It’s more challenging to deploy the OS X platform in other areas,” says enterprise architect David Lee, although Genentech does support some Macs that need access to Windows applications by using virtualization software such as Citrix XenDesktop or VMware Fusion. That software layer, however, adds complexity and cost.

“Our No. 1 recommendation is to look at the applications first,” Silver says. “If users need access to Windows applications, they should be running a Windows machine.”

Mike Reed, an Apple solutions practice manager at IT services provider Forsythe Solutions Group, sees it differently, arguing that having parallel applications isn’t always necessary. For example, Microsoft Vizio files can be read by OmniGraffle on the Mac. “It’s less about the app and more about interacting with the data,” he says.