Well -- you should listen to your compiler -- it is correct.
When you have a 2D array (which is actually and array of array double [3]), on access, the first level of indirection (the first [..]) is converted to a pointer to the first element. So double arr[2][3]; is converted to a pointer-to-array double[3]. (a pointer to the first array of the 2 double[3] arrays). The type for a pointer-to-array double[3] is double (*)[3] -- just as your compiler is telling you.
To make things work correctly, your prototype should be:
int numberNegative (double (*arr)[3], int r, int c);
Then within your function, you can count the number of negative values with:
    for (int i = 0; i < r; i++) {
        for (int j = 0; j < c; j++) {
            if (arr[i][j] < 0)
                counter++;
        }
    }
    return counter;
Note: j < c NOT j <= c (which exceeds the bounds of the array by 1) and no if (arr[i] < 0) counter++; which attempts to compare an pointer to double to 0. 
Further, you cannot have return counter; within your for loop and expect to return the correct value for all negative values in your 2D array. Where you do:
for (int i = 0; i < r; i++){
    ...
    return counter;
}
You need to move return counter; out of the loops to the end (last statement) in your function.
There is no need for a global int counter; and see Why is “using namespace std;” considered bad practice?
Putting it altogether, you would have:
#include <iostream>
int numberNegative (double (*arr)[3], int r, int c);
int main (void) {
    double data[2][3] = {{-3.0, 1, 4.5}, {-2.2, 7, 1.4}};
    std::cout << numberNegative (data, 2, 3) << '\n';
}
int numberNegative (double (*arr)[3], int r, int c)
{
    int counter = 0;
    for (int i = 0; i < r; i++) {
        for (int j = 0; j < c; j++) {
            if (arr[i][j] < 0)
                counter++;
        }
    }
    return counter;
}
See also: C++: “std::endl” vs “\n”
Example Use/Output
$ ./bin/count_double_neg
2
Which corresponds to -3.0 and -2.2. Look things over and let me know if you have any questions.