There is really no way to make a secure bed cover. They do hide what's inside and make theft a bit more difficult than reaching in an open bed and grabbing something. If a real thief sees what you have and wants it ... byebye.
So you're stopping casual theft by people who have no qualms about stealing low hanging fruit, or addicts who need something - anything - to pawn. I think the prime use of a bed cover is to get a reasonably dry cargo area without the "soccer mom" stigma that comes with a minivan or the hassle of a full size van that won't fit in most parking structures.
Professional thieves - meaning they live off the job - don't crack open truck beds hoping to find something worth stealing. They find out where valuables are and then get them. The typical locks on truck bed covers are a moments work to pick open for even a neophyte lockpicker. Most cars or trucks can be opened in minutes with no evidence or damage, in seconds by breaking a window.
So don't worry, be happy.
How often do you carry a bike or other large items? Hard shell covers come off fairly easily with two people but need a spot to store it. Roll ups have major leak problems so if you need the bed go be dry that is not great. Tonneaus keep weather out pretty well and are easiest to open up.
