There has been no shortage of speculation since news broke that Apple's M&A representative spoke with Elon Musk about acquiring the increasingly famous auto maker. Josh Ong has made a great case for why it might make sense, so I won't duplicate that.

The whole issue has some red flags that stand out to me as pretty major reasons an acquisition wouldn't happen.

The auto industry is a low margin industry, especially on the low end. Tesla is not yet competing in the lower end market, so their margins are likely much closer to Apple's than Hyundai's, but Tesla has plans to expand into the $30,000 arena where there is simply no way to have Apple-like margins.
The whole situation seems Google-y. Apple's wheelhouse is making beautiful and simple computing devices. An entry into the auto industry, despite Jobs' reported desire to do so, is un-Apple-like. With that being said, the auto industry is so slow to adopt new technology that it would be quite easy to disrupt.
Setting aside the magnitude of the purchase being vastly beyond anything Apple has purchased before, the fact that they couldn't make this purchase quietly is worth mentioning. Apple tries to keep those as quiet as they can, this one would be making headlines around the world.