It isn't so much for the boot time, but the application load time, and general system responsiveness. When you have an SSD bogging down your system is hard to impossible to do. Even if multiple things are launched at once it doesn't impact your ability to use it because they service simultaneous requests much better. Likewise programs load lightning fast. I play a lot of video games and it is great not having to wait on loading screens, stuff just comes up nearly instantly.
Also the thing is you often have no need for the storage capacity of a magnetic drive for a boot/apps drive. 1TB is more than most people would use for that purpose. So comparing a 500GB SSD to a 1TB HDD actually makes sense since the SSD is plenty large enough. As a simple example I have a 512GB system SSD and I have only about 200GB used. On it I have my OS, Sonar, Vegas, Soundforge, associated audio plugins, Office, browsers, editors, and a number of games including Dragon Age Inquisition, Final Fantasy 13, and Shadowrun Hong Kong. I have a fair bit of stuff, and yet it all fits nicely on an SSD, and would fit fine on a 250GB SSD in fact.
So ya, you can get magnetic drives for less, nobody questions that, and for bulk storage SSDs are way too expensive. But OS and apps work pretty nice on a smaller SSD and then your system is just extremely zippy.