My Bunny was neglected and only on pellets for about 5 years (before I got him). When I pat him he often lays down (legs underneath him), is that good? Also, how do I get him happier? He is free roamed, gets vegetables, lots of love but doesn't play with any toys.
Bunnies laying down to pancake are a great sign, it means they are comfortable.
Rabbits do need enrichment items (toys), but not all rabbits like the same toys. My former rabbit loved fling toys--things like baby toy keys that he could throw with his mouth. My current rabbit doesn't really like those; she prefers chew toys such as willow balls and loves running around her tunnel.
Here is a great resource on how to win over a shy rabbit if that is something you are still concerned about.
Bunny lays down (like a pancake) when I pat him
I am not sure what you mean by 'pat', if you mean the verb 'touch quickly and gently with the flat of the hand' then you are doing it wrong.
Bunnies like to be stroked. Soft pets that glide easily over the fur. I go into some detail in this answer.
As for playing with toys:
Cats and dogs like to chase things (think catch and eat prey).
Rabbits don't chase things, they will occasionally toss things. But they play different than cats and dogs. They like things to chew on and dig in.