Right, but if he had teammates that could just gank him, he wouldn't have an issue with him.
Basically, it's all about pushing fast and denying his early game. Because midgame with a little farming(mana regen and cooldown reduc gear) his harassing increases considerably, this is usually the time people have issues with.
If he's running in to drop a bomb on a player, make sure that player runs away from the minion packs. Reduce his mana effectiveness by forcing him to choose between hitting -1- player, or minions. And don't drag bombs onto other players, it's not nice.
Sidenote, I've seen Zileans with smite, they love to drop a bomb on a minion near you then smite it immediately to harass. Keep an eye out for this tactic.
An early Wit's End or diff mana drain can shut him down. Zilean has LOTS of mana issues, watch his mana like a hawk, because his auto hits like a sock, and if he has no mana, he's literally an old guy strapped to a clock, kill him with impunity.
Right, yeah, I hate gearing against specific heroes, but a Negatron cloak will cut a LOT of damage off his bombs. But if you're gearing SR, you need to have a teammate that can compensate for the DPS loss, otherwise you probably won't put him down.