Errors and warnings are printed to stderr.

Fixes https://github.com/aws/aws-cli/issues/820

cc @jamesls @danielgtaylor 
Why do we want to not return after this line?  Do we still want to print the progress on an error?  For example:

```
$ aws s3 sync . s3://bucket/syncme/
warning: Skipping file /private/tmp/syncme/baz. File/Directory is not readable.
Completed 0 part(s) with ... file(s) remaining
```

Looks a bit off to me.