Not if you know what you're doing. For example, say you added a bunch of TODOs and FIXMEs you noticed in existing code while working on something. Now, you're ready to commit. The TODOs and FIXMEs don't necessarily correlate to the code changes you made. Should they all be committed with the code?

Using the index to stage and commit hunks separately lets you easily add and commit the unrelated TODO and FIXME comments separately from the code. A tool like Magit makes it trivially easy to do.

And since they're comments, they have no effect on tests or the code.