Apple Inc. (NASDAQ:AAPL) investors are worried about many things. The stock’s relative under-performance in recent times, despite a ridiculously low valuation and continuing growth, seems inexplicable. A new analysis from Bernstein Research seeks to take at least one worry from the minds of traders; Apple Inc. (NASDAQ:AAPL) iPhone margins are going to be fine.

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The common argument about the inevitable reduction in iPhone margins is attractively simple. Just like the PC market, increases in specs are likely to become less and less important as performance in everyday tasks flattens out. Once that happens the market is commoditized; there’s little difference between products for consumers and margins disappear.

Apple iPhone is not a commodity

There is a clear problem with this analogy, and Bernstein analyst Toni Sacconaghi, Jr. does well to point it out. Apple Inc. (NASDAQ:AAPL) is already in the PC market, and their line of computers, the Macs, has not been commoditized. Its margins remain healthy and consumers see Macs as very different from other computers.

There are many strengths at Apple Inc. (NASDAQ:AAPL) that make this possible. The company has an incredibly strong brand, and it operates inside its own ecosystem. Macs have their own distinctive design and feel, and they have certain software unavailable on other computers. The iPhone can be the same, despite the changes in the smart phone market.

Gross margins at Apple Inc. (NASDAQ:AAPL) have, however, fallen in recent quarters.  Recent theories posit that iPhone margins are cyclical, and will improve in future. The current lull in margins is due to the specific design of the iPhone 5, rather than a secular trend toward margin compression, according to that theory.

Apple is not just another phone maker

There are many reasons to think that the Apple Inc. (NASDAQ:AAPL) iPhone can manage to retain the same general margin level over the coming years. The product has an exceptionally good brand, and its customers tend to be fiercely loyal. Apple Inc. (NASDAQ:AAPL) is not just another phone maker, it’s the only company that makes an iPhone. That means its margins might be safe.

The Bernstein analysis certainly points in this direction and provides a major impetus for the Outperform rating put on the company’s shares in this report. The report puts a twelve month price target of $600 on Apple Inc. (NASDAQ:AAPL)