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In a blog post, Marco Arment, the app's creator, writes:
I’m happy to announce that I’ve sold a majority stake in Instapaper to Betaworks. We’ve structured the deal with Instapaper’s health and longevity as the top priority, with incentives to keep it going well into the future. I will continue advising the project indefinitely, while Betaworks will take over its operations, expand its staff, and develop it further.
Arment explains in his post that he figured out a couple of months ago who should acquire his app and shot off an email late at night. Both Arment and Betaworks mutually agreed that the acquisition was a good fit.
Betaworks is an incubator that starts companies and aims to make them bigger. It's the same company that acquired Digg last year.