The stealth operations began during George W. Bush's presidency and have expanded under Obama.

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he Obama administration is conducting a "shadow war" on al Qaeda and its allies in a dozen countries, from Yemen to Pakistan to several former Soviet republics, according to a report in The New York Times. The stealth operations, which include intelligence gathering and drone strikes, began during the presidency of George W. Bush, but it have been expanded under Obama. The program amounts to using a "scalpel" rather than a "hammer" to fight terrorism, says John O. Brennan, Obama’s top counterterrorism adviser. Is this new approach making America safer? (Watch a CNN discussion about Obama's "secret" war)

Sounds like an effective way to fight terrorists: "I like the idea of using a scalpel rather than a hammer," says James Joyner at Outside the Beltway. It means the fight against al Qaeda won't end after the Afghan surge is over and the Iraq drawdown is complete. It also means that despite the right's fear that Obama is "a secret pacifist who wanted to end the war on Islamic extremists," he's actually continuing Bush's national security policy with "nuanced differences."
"Obama's shadow war on terror"

We're driving recruits into al Qaeda's arms: This shadow war isn't making Americans any safer, says Jeralyn Merritt at TalkLeft. Airstrikes in Yemen, some of them botched, haven't eroded al Qaeda's capabilities in the region, and appear to be helping terrorists convince recruits they're fighting a heroic struggle against American aggression. "Instead of ramping up military strikes we should be providing developmental aid" to reduce the poverty that feeds terrorism.
"Obama administration's expansion of the war on terror abroad"

Exposing the secret war is what helps the enemy: If liberals are worried about creating more terrorists, says William Teach at Right Wing News, why is a liberal newspaper like The New York Times blowing the lid off Obama's secret war? Recklessly exposing our clandestine operations in Yemen "could do irreparable harm to our dealings" with that country's government, and further inflame a population already "ripe with hard core Islamists."
"NY Times exposes yet more secrets from the war against terrorism"