They'll be fine. Isolate them for a few days right after they hatch--it'll give them a bit to work out who mommy is and what her clucks mean and then they should be fine with the rest of the flock. Hens don't like chicks, but they won't bother the hormonal monste--mother. I mean 'mother.' Roosters usually don't bother chicks at all and often are quite fond of them.
Sometimes, the momma makes enemies by attacking everything in sight and there will be some truly epic barnyard battles. I usually isolate for a few more weeks if that happens, but I've never actually had a chick injured in the battles. stepped on, yes, injured, no.
Broody hens will peck at each other's chicks, but the chicks soon work out whom to avoid.