First of all, let us to get clear which exactly are the MySQL functions. link

So why I say that they are bad to use? Well I personally do not. PHP is changing, so is every other language. After about 10 years of successful usage, these functions are officially deprecated and some day they in the bright future they will be removed.

What should I use then? There are many other ways to manage your database. Php.net suggests us to use the MySQL Improved Extension and PDO (PHP Data Object). Not to mention what kind of advanced ORMs (Object-Relational Mapping) exist.

Try not to use these functions anymore. With some little bit of digging into, for example, PDO you will understand the difference and you will not regret for doing so.