The AWS CLI and AWS CloudFormation are two different tools that can be used to create infrastructure on AWS. The CLI is more powerful and has finer grained control than CloudFormation. CloudFormation makes it very easy to use yaml or json text files that can describe an entire enterprise in the cloud.
One of the strong benefits of CloudFormation is the automatic support for rolling back changes if anything fails while deploying a stack. The CLI in comparison would require you to figure out the details of what went wrong and how to get back to where your state was. Updating infrastructure using CloudFormation is another benefit. Make the change in the template and update the stack.
For small setups, using the CLI is fine. However, once you get past launching an EC2 instance and start building VPCs, Instances, KeyPairs, Security Groups, RDS, etc. etc. you will find that the CLI has some real limitations: mostly being too manual of a process, not easily repeatable, difficult to put the process into version control, ....
If you are constantly building, testing and deleting complex setups, CloudFormation is absolutely one of the best tools from AWS. Note that there are a number of third party solutions that have a huge number of followers such as Bamboo, Octopus, Jenkins, Chef, etc.
If your job is SysOps or DevOps then you absolutely want to master the CLI and CloudFormation. These are amazing tools for working with AWS. Also master Beanstalk, maybe OpsWorks and one of the third party tools like Jenkins.