The problem is that the AI refuses to send a settler alone on a ship, correct? Some options:
1) AI gets the cargo promotion for free on all ships built. This could be unpleasant if they go to war with you. And would allow ships that have 0 capacity to have 1 right off the bat. But could be an easy thing to try.
2) AI gets a free special promotion that is +1 space if space is exactly = 1. Might be too complicated. But would be better than (1). 0 space ships would not get free cargo, for example.
3) Weight the capacity upgrade on ships higher. Then if the AI has a couple experience on a ship, it will take cargo as the first promotion. Ships would be weaker though.
4) make unit size fractional. Normal units are size 0.9, settlers are size 0.1. Doesn't make sense, but would allow 1 unit + 1 settler to fit in a capacity 1 ship. Could then make giants, elephants, and maybe cavalry size 2

But that is probably too painful in terms of coding.
Actually fractional is just too silly. Maybe instead, have AI settlers take no space on ships (Promotion="really thin", lost on unit capture, where they convert to workers). Special promotion maybe? Problem with special promotions -- you probably want to make sure they aren't available for mutation.