There are a lot of differences between the two: MTB's and ATB's...

ATB's Crank - 48-38-30/28
MTB's Crank - 44/42-32-22

ATB's Drive System - Usually 7speed
MTB's Drive System - Can Be 8 or 9speed

ATB's Cockpit/Handlebars - Very upright, with a 25* or more angle on the stem
MTB's Cockpit/Handlebars - Usually Neutral or level with the saddle or under the saddle for a faster more aggressive stance

ATB's Rims - Mostly Single Walled
MTB's Rims - Mostly Double Walled and may even have reinforced eyelets

Bottom line:

Both will accept a host of upgrade parts - there is plenty of Braze-on mounts for Racks, Fenders, and the like...

ATB's are great for Greenways and School Campus' because they cruise out more upright, and their cheaper spec' makes them easier to replace when/if they get stolen. They have their place - just not on the trail.

MTB's are great for Offroad Trails and Fast Commutes ranging from 3 to 10 miles. Their more durable spec' leaves them looking for longer more frequent rides due to the increased durability. Around a lot of traffic though and you MAY find a sore neck from having to look out to a further than normal event horizon.

I hope this helps you out!