If you're following the protagonist, which is usually the case, then normally that protagonist is portrayed as good in some sense or has some redeeming qualities otherwise you could not sympathize with the protagonist.
As such, logically an alter ego would offer an alternative version of that protagonist, and although an alter ego doesn't have to be darker, it is usually the case, since otherwise you'd risk that readers would sympathize with the alter ego instead. For the same reasons, doppelgängers are often seen as evil versions of the protagonists.
This isn't to say there aren't exceptions. One exception that comes to mind is Dexter, whose alter ego is a forensics analyst for the police when really he's a serial killer. Interestingly, he himself is dark and his alter ego is the mask he puts on for others to see.
An interesting quote I found from Quentin Tarantino on the subject:
“Superman didn't become Superman. Superman was born Superman. When
Superman wakes up in the morning, he's Superman. His alter ego is
Clark Kent. His outfit with the big red "S", that's the blanket he was
wrapped in as a baby when the Kents found him. Those are his clothes.
What Kent wears - the glasses, the business suit - that's the costume.
That's the costume Superman wears to blend in with us. Clark Kent is
how Superman views us. And what are the characteristics of Clark Kent.
He's weak... he's unsure of himself... he's a coward. Clark Kent is
Superman's critique on the whole human race.”