Yes, sort of.
The Flight hex allows you to fly as if using the spell Fly. Thus because Fly grants a bonus to Fly checks equal to half the spells caster level, this also applies to the Flight Hex.
Note however that the Hex Witch class feature nor the Flight hex itself specify what the caster level is for Fly component of the Flight hex (opposed by the Healing hex, which does specify a caster lv). This is important because the Fly spell's bonus is dependent on caster lv.
Though quite frankly, it's probably safe to assume the caster level is supposed to be equal to the Witch's class lv.