USA Today’s new publisher David Hunke regrets not charging for its iPhone application, even though mobile phones and portable electronic reading devices continue to be an opportunity for new revenue sources.

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“I’m not sure we realized what we had,” he told AP. “I think that’s a value readers will be willing to pay for.” USA Today is not only giving its content away on the iPhone, but also Google’s Android device. The plan was to make money through advertising, such as click-to-call, click-to-maps using the user’s GPS location, and video. But that must not be working out so well. USA Today should think about reclaiming some of its higher-end content that its giving away for free and providing it separately for a monthly subscription, which is a new billing capability that Apple (NSDQ: AAPL) is rolling out with the 3.0 operating system on June 17. See our sister site paidContent.org for more on Hunke’s plans for making money.