While I strongly believe that scientists should publish their code along with their papers, I do think it has one potential disadvantage. Suppose a scientist writes a big piece of code to some complicated calculations, but makes a subtle mistake somewhere in it (perhaps some parentheses are nested incorrectly). If the code is not published and another scientist comes along to extend the results from the first paper, the first thing he will do is try to replicate the results of the original. If the code is unpublished, the second scientist will have to write the code from scratch, and in doing so will likely catch the original error. But if the code is published, the second scientist will just use the original code and probably won't catch the error. Consequently, the mistake will take much longer to catch, if it's ever caught at all.

The advantages still outweigh the disadvantages, but it's important to remember that there are always trade-offs.