homestead already has a cron job running every minute, which executes schedule:run (which is how it is supposed to be). You shouldn't have to enter anything in cron.
You just need to schedule a job through the scheduler using ->dailyAt('00:05'); if you want it to run at 5 after midnight.
I guess remove the default cron job that's running every minute. But then you'd lose the whole purpose of having cron jobs in code as opposed to crontab and would have to create and maintain each cronjob on each server manually. It's much better to have it in code so it's a part of your repo, and you only ever need one actual cron job to execute all jobs no matter when they were.
You could also check the current date/time to see if it matches your $time in your loop, and execute the scheduled command if it is. That would allow you to keep everything in code still and do what you are wanting.