Can neurogenic atrophy in thenar muscle from nerve injury cause als? or does it only apply to those with nerve disease?

No: The cause of ALS is unknown. Injuring a nerve is not associated with ALS. Muscle atrophy is seen in the affected areas of ALS. If there had been no injury and you developed muscle wasting for no reason, ALS, would be considered as a diagnosis. there is a nice review in Wikipedia: http://en.wikipedia.org/wiki/Amyotrophic_lateral_sclerosis

Prob not ALS: Thenar atrophy is normally caused by median mononeuropathy, aka carpal tunnel syndrome. Other causes are relatively rare. ALS may cause thenar atrophy, but since if affects multiple nerves and muscles, this should not be the only sign or symptom. Of course, thenar atrophy does not cause ALS.