RadioRon makes some good points, here are a few more:
Proto boards are also cheaper in small quantities, easier to modify and quicker to build (usually). I always keep a small supply of proto boards on hand for small projects, and find they're usually a good choice for most projects.
Generally proto boards are a good choice with an initial design, this is especially true if you might later modify it ...and yes you will modify it
With circuit board manufacture. there's either etching it yourself, or paying to have someone else etch it. If you do it yourself you have etchant to deal with, board design, layout etc. If you have a PCB manufacturer make your board(s), you pay to have boards made and there is also a slight delay in receiving your boards. If you don't discover an error, until after you get the boards back, you're stuck with them. On the plus side, a commercially made PCB looks much nicer than either a protoboard or home etched PCB.
A PCB is a good choice after you've perfected your design, and can be much quicker to assemble, especially with multiple boards.