It is possible to calculate the co-occurrence matrix in WEKA assuming you have binary data. (If the data is not binary, you will have to use the MathExpression filter to binarise the data first.)
The idea is to first take the transpose of the data matrix and then apply the KernelFilter with a dot product kernel (the default), turning preprocessing in the kernel filter off.
Here is an example input dataset in CSV format:
product1,product2,product3 0,1,1 1,1,0 0,0,1
Assuming this data is stored in a file called test.csv in the current directory, the co-occurrence matrix can then be computed by using the following command-line if your operating system supports piping with the "|" character: