Sending SMS (Short Message Service) with PHP application is done for multiple purposes. For example, many security enhancements are integrating multi-factor authentication system where you can additionaly identify user by mobile device, retrieve forgotten passwords or similar. Other common usages are sending marketing messages, or notifing users about different events and similar.
The diagram below explains a simplified SMS sending flow where PHP application communicates with a SMS gateway. Gateway converts and forwards received data to SMS center (SMSC). SMSC routes data to mobile device (end user).
Most common and simple to integrate usage in PHP applications is using an SMS API.
Another, less common and less stable option to send SMS is using an email from particular carrier. SMS is sent by sending an email to certain address with predefined email data.