I also read a lot of blog posts and heard stories about bus travel in Peru being dangerous.
However, all the ones I was on were pretty good. I travelled in semi-cama and full-cama class, with a variety of companies. No problems with any, and most were pretty good at being on time, unlike a couple I had in Argentina.
I travelled at night from Cusco to Arequipa, Arequipa to Lima, Lima to Mancora and up to and crossed the Ecuadorian border at night too. No problems at all.
I heard the same about Colombia too, people were shocked that I'd travel, but think logically - these buses go through these areas every single day and night, several companies. If there were problems every day, it'd be in the news. It'd be huge.
This doesn't mean you will be fine. Odds are you will be, but accidents do happen occasionally, everywhere. Be aware, keep your valuables with you (and NOT under your seat), and when possible, travel with someone else as well, or get to know the people around you.