Can a prepositional phrase be the direct object?

I think you see the whole thing totally wrong.

A direct object never has a preposition.

• I'm reading a novel - a novel is a direct object. You ask: What am I reading?
• I'm waiting for the bus - for the bus is a prepositional object You ask: What am I waiting for?

In your sentence "Pilgrims learned about planting crops from the Wampanoags." "about planting crops" is a prepositional object and "from the Wampanoags" is a second prepositional object.

Maybe English grammars have other terms, but that's the way I see it.

"learned about" is a phrasal verb -- see http://en.wikipedia.org/wiki/Phrasal_verb

Pilgrims = subject noun

learned about = phrasal verb

learned about what? planting crops

planting = gerund (Present participle verb form used as a noun - in this case the direct object.)

crops = gerunds may have their own object