It's possible that he might have taken an investment from someone that does not take failure/underdelivery as an answer. Or that Gokada's continued existence pissed off someone that intended the company to go under. It could also possibly be much more personal than that - there are many people who are wealthy enough to order such a hit with relative impunity (as long as they remain in Nigeria - our justice system and infrastructure is frankly not the greatest). It could also have nothing to do with Nigeria at all; he had business ventures and personal affairs elsewhere.
It's all speculation at this point and I just hope whatever it is doesn't crush the company. Gokada employs a thousand riders but beyond that it's helped so many small businesses grow and thrive especially during this period; there's a huge informal vendor culture in Lagos that's enabled by companies like this.