fsck ("file system check") is for repairing structural damage to a file system, which might result from a crash. (Unless you use the new journaling feature!)
The more likely trouble you'd get into playing with the CLI (command-line interface) wouldn't be repaired by fsck. For example, if you delete or move a file that is critical to the operating system, you might not be able to boot or run your applications and fsck wouldn't help. You might need to restore from a backup or reinstall Mac OS X.
The command-line power of all Unix variants, including Mac OS X, comes from the ability to combine dozens of powerful commands in any way you can think of. That power is the beauty and also the danger. You can, for example, use a single command to scan a directory and its subdirectories for files with extension .txt that were created in the last two days and contain the word "poiuyt", sort the list by filename, create a tape archive (tar file) out of them, compress the tar file, and store it somewhere. On the other hand, you can just as easily wipe out all the files in the /System/Library folder, trashing Mac OS X in the process.
You are more likely to stay out of trouble when you confine your activities to files in directories (folders) that you create yourself or when you play with applications and files that you can reinstall or recreate if necessary.
The same goes with using shell scripts, AppleScripts, C++ programs, etc. You'll gradually learn to use your superpowers for good instead of evil!