Many factors will be there and some time in Industry I have cases like they are simply have high rates just because they have enough clients which is having no issues which normally are some country limited or local limited hosting company and clients may be mostly unware of the Industry rates and standards. 
But normally the below is the main things we need to consider
1. Extra Paid softwares provided for the customers like the below 
Website Builder, 
Easy Software Installer like Softacuilous/Fantastico, 
Whether Litespeed is used or not  
Whether extra security plugins are used 
2. Extra amount is spend on the Server Hardware costs like 
Raid 10 
Backups server / Backup drive
More number of backups available 
3. Quality of the Support  like 
24/7 real support staff is available
Lesser delay in Response in tickets 
24/7 livechat is available or not 
4. Datacenter on which they have their server and its Standards like Tier 3 Tier4 etc and goes on. 
For VPS, normally I have see some give the below as free but in short all are almost paid but will have that fee covered in the rate for sure
free Blesta/whmcs 
Free Domain 
Free SSL 
Managed Support 
In short there should be some profit as it is business and the rate will be dependent on that. 
It is simple business in the end  
