Instead of "protecting" some kinds of expressions, you could just explicitly specify that you only want to replace products with integers:

Replace[ 4 x^2 (4 Subscript[a, 1] + Subscript[a, 2] - 7 Subscript[c, 4]), n_Integer a_ :> 2 n a, All ] 

Instead of "protecting" some kinds of expressions, you could just explicitly specify that you only want to replace products with integers:

Replace[ 4 x^2 (4 Subscript[a, 1] + Subscript[a, 2] - 7 Subscript[c, 4]), n_Integer a_ :> 2 n a, All ] 

This way, you don't risk forgetting to protect some form of expression