One selling point of Confidant is using IAM roles to bootstrap authentication to the secret store. You can also do that with S3, put each secret into an individual text file and give each IAM role permission to access the secrets it needs. Set the S3 bucket to encrypt the data at rest, it uses KMS behind the scenes and automatically rotates encryption keys.
Rotation of the secrets themselves could be scripted or manual, that part would be basically the same process as using Confidant or any other tool. And I believe S3 access can even be auditable with CloudWatch logs.
Also, S3 now offers either eventually consistent or read-after-write consistency. EDIT: actually, it looks like new object PUTS can be read-after-write consistent but updates are not. So this could be a downside, if you rotate a key getting the new one is eventually consistent. In practice this might not be a big deal though, there's already going to be a gap between when you activate the new key and when your app gets reconfigured to start using the new key.
I'm very curious what the downsides might be of doing this. For all the various secret management tools that have been released in the past year or two, I'm kind of surprised I've never heard anyone talk about using raw S3.
Confidant provides access to credentials by IAM role. The key here is that you can have credentials A, B, and C, and IAM roles example1-production, example2-production and example3-production, then map credentials A and B to example1-production, A and C to example2-production and A to example3-production. Confidant just stores mapping info for this. If you update A, you don't need to fan out an update to all three services. Race conditions can come in when A and B or C are updated at the same time. S3 is very eventually consistent and there's no locking. read-after-write consistency is only available in one region at this point.
Of course, this is all based on your assumptions and how you design your system. Based on our needs KMS + DynamoDB made more sense for us. Something like sneaker (https://github.com/codahale/sneaker) may fit your needs better.
Another interesting bit about Confidant is that it manages the KMS grants on the auth KMS key, which lets you use the key from any service to any service to pass secrets, or to do general service to service auth.
Also, there's a bit more coming down the road for automatic management of other common secrets that are annoying to manage in AWS, like SSH host keys for autoscale groups: https://github.com/lyft/confidant/issues/1