Creating a 2D array from a txt file
Consider using Arrays.asList("", ...) to create lists in-line.
Why are colors and models Lists while cars is an Array? It seems like you can use Arrays for all of this.
Consider using "anonymous arrays" (terrible name) to create Arrays in-line. 
Consider first building the "true" data structure as int[][] car_counts = new int[7][7], a zero-indexed 2D array of counts. Then treat the task of printing it as shown in the image as a separate problem. 
Your while loop at the end appears to be incorrectly indented.
That while loop should be building a data-structure that you can neatly read the file into: a list of pairs of strings. (or even a list of pairs of ints, representing indexes into models and colors.)