Query builders are a pet hate of mine, so much so I wrote my own Framework (Apeel) to avoid using them!
If you use PDO (which I definately recommend you do) then santising the input is handled for you.
Like someone else said, although they do make it easier to switch between databases they tend to support "Lowest common denominator" functionality and will either not support or have poorer performance for more advanced features.
I've been developing systems with databases since around 1986 and in all that time I've rarely encountered a company actually changing the database they use other than when they needed better performance. If you are changing databases for better performance then it makes a lot more sense to spend your time hand-optimising your queries to get the best out of the new database rather than take the hit of a query builder for the sake of simplicity.
The time spent getting to grips with the qwirks of a query builder (then re-learning when you switch to a better one) would be far more productively spent learning how to optimise your SQL.
Anyway that's why NOT to use one, some people love them though.