Judging from the map found on the Beechcraft in "Deus Ex Machina" the plane may have been headed towards Inedbirenne Airport in Algeria (24 17' 31" N, 9 27' 08" E) which is roughly halfway between Nigeria and Tunisia, where the Polar BearJohn and Ben was transported.
Tunisia is a logical destination for drug smugglers, since it provides easy access to European ports. Also, Tunisia's former president, Zine El Abidine Ben Ali, was long rumored to be involved in the drug trade.See BBC
Cause of Crash
If Mr. Eko's brother Yemi died while the plane was airborne, his spirit/ghost could have caused the crash in an effort to help Mr. Eko after having learned of future events. We can assume Yemi's spirit/ghost has some knowledge of the future. In the episode "?", Charlotte Malkin tells Eko what Yemi told her while she was between places, including 'seeing him soon'.
The Island was in a different location when the plane crashed on the Island.
An airplane of that type, carrying cargo and not loaded with extra fuel tanks would not be traveling far enough from land to encounter an uncharted island. They took off in full daylight so the diversion to the island suggests supernatural intervention.