I've thought about giving other runners a "Keep it up" in the past but opted not to as I feel it's unintentionally condescending.
My reasoning is that I'd never encourage an athlete or someone I determine to be better than or equal to myself at running, so why would I feel it's okay to give words of encouragement to someone just because they're slower than me or an obvious beginner.
For example if I saw someone running 1 mile 5 minute repeats at my track, I'd never try to get their attention or yell encouragement at them. So why would I do that to someone anyone else when I have no idea how much effort they're putting into their run.
At most I say "Hi" or nod my head if it's someone I cross paths with on more than one occasion.