Here is a really simple example for ROT13 cipher. Used for demonstation purposes only. Made to be as readable as possible.

Rot13.c

#include <stdio.h> /* putchar, printf */

void printRot13(const char* str)
{
  /* loop through string. Strings end with a \0 */
  for(; *str != '\0'; ++str)
  {
    /* If letter is in the lower 13 letters, add 13 */
    if      (*str >= 'A' && *str <= 'M') { putchar(*str + 13); }
    else if (*str >= 'a' && *str <= 'm') { putchar(*str + 13); }

    /* If letter is in the upper 13 letters, sum 13 */
    else if (*str >= 'N' && *str <= 'Z') { putchar(*str - 13); }
    else if (*str >= 'n' && *str <= 'z') { putchar(*str - 13); }

    /* If the letter can not be encrypted *
     * print the original letter          */
    else { putchar(*str); }
  }

  /* Add a space between words */
  putchar(' ');
}

int main(int argc, char** argv)
{
  /* Check to see if there is any input text */
  if(argc == 1)
  {
    /* Print error if there is none */
    printf("%s: No Input Text!\n", argv[0]);
  }
  else
  {
    /* Loop through all the inputs *
     * and encrypt them all        */
    for(int i = 1; i < argc; ++i)
    { printRot13(argv[i]); }

    /* Print new line, for the shell */
    putchar('\n');
  }

  return 0;
}