Allow me to introduce you to the Diesel Tree, a tropical plant that naturally produces some petroleum-like precursors (turpenes). It's not exactly high yield, but it is a fuel source that literally grows on trees.
Public Domain - By Mauroguanandi
Seeing as there's no "hard science" tag, and we're talking about people who can terraform whole planets, I'd recommend a genetically modified version that has both a higher oil yield and a wider climactic range (seeing as it can't be "the tropics" everywhere). If you need a reason to have the trees pre-apocalypse, well even today, there's a lot of non-fuel things made from petrochemicals, so it'd be useful to have a low-maintenance self-sustaining source (especially on a frontier world)
N.B. if you want a purely organic solution, you're going to have to come up with a work-around for the fact that the world of today is chewing through our fossil fuels many, many, orders of magnitude faster than they were laid down to begin with. You'll probably have to accept a limited, albeit renewable, supply of fuel until civilization is able to build some solar panels and electrify everything.