has_and_belongs_to_many is meant for simple many-to-many relationships.
has_many :through, on the other hand, is meant for indirect one-to-many relationships, or many-to-many relationships with properties.
If you're only looking for a simple many-to-many relationship, I can't see any reason not to use has_and_belongs_to_many.
Example many-to-many relationship:
User belongs to zero or more groups, and group has zero or more members (users).
Example many-to-many relationship with properties:
User belongs to zero or more groups, and group has zero or more members with ranks.
For example, Alice might be an Administrator in Group A, and a Moderator in Group B. You can hold this property in the join table.
Example indirect one-to-many relationship:
A category has zero or more sub-categories, and each sub-category has zero or more items.
A category therefore has zero or more items through its sub-categories.
Consider these categories:
Food → Fruits, Vegetables
Fruits → Apple, Orange, etc.
Vegetables → Carrot, Celery, etc.
therefore:
Food → Apple, Orange, Carrot, Celery, etc.