I would guess that it is a way to make applications which don't use it at all perform slightly better. Here's my thinking on this.
x86 OSes (and I imagine others) need to store FPU state on context switch. However, most OSes only bother to save/restore this state after the app attempts to use the FPU for the first time.
In addition to this, there is probably some basic code in the math library which will set the FPU to a sane base state when the library is loaded.
So, if you don't link in any math code at all, none of this will happen, therefore the OS doesn't have to save/restore any FPU state at all, making context switches slightly more efficient.
Just a guess though.
The same base premise still applies to non-FPU cases (the premise being that it was to make apps which didn't make use libm perform slightly better).
For example, if there is a soft-FPU which was likely in the early days of C. Then having libm separate could prevent a lot of large (and slow if it was used) code from unnecessarily being linked in.
In addition, if there is only static linking available, then a similar argument applies that it would keep executable sizes and compile times down.