One big hangup users have is a difference in expectations. They know what they're getting with the money they pay towards their iPhone. Heck - most users will gladly pay exorbitant prices for a cup of coffee as long as it meets their expectations. The same cannot be said for a given app they pull off the App Store. The quality experience can vary greatly from app to app. Even then, an app that fits your lifestyle may not fit mine, so a recommendation isn't necessarily a guarantee of value.
For me I think it is a question of ownership. It is easier to pay for something you actually own. Software already is intangible, but add in modern licensing, app stores, etc and you really do not have any ownership over your software. Even in the case of open source software like signal, Apple could chose to boot them off the app store tomorrow and I would lose my "investment".
There was a time in the 90s/00s where you bought software in a big box, and it came with all sorts of manuals and such. The tangible assets (manual, floppy, box, whatever) along with the licensing agreement made that software much more valuable than the software we use today.
I remember when some of them came with hardware dongles. Adobe After Effects had a dongle that you had to attach to your keyboard cable in order for the app to launch. The mental value I attributed to that dongle was immense. I think I still have it around here somewhere...
I'd venture to guess that speed/simplicity of installing an app is also something users subconsciously factor in. The faster/smoother the installation, the less appreciation they have for the app. I remember installing Windows 95 from floppy disks.. boy oh boy, I appreciated every file that was successfully installed and admired it every time it booted into desktop.
