Does a creature with wither deal -1/-1 counters when dealing damage through trample to a player?

Wither (CR 702.90) states that a source with wither deals damage to creatures in the form of -1/-1 counters instead of marking damage. This replacement effect only applies when the damage recipient is a creature.

When a creature with trample attacks, the attacking player must assign lethal damage to each blocking creature first, then may assign the remaining damage to the defending player or planeswalker (CR 702.19b). The portion of damage that "tramples over" to the player is still damage — but wither's replacement effect does not apply because a player is not a creature.

Damage dealt to a player simply causes that player to lose that many life points (CR 119.2), with no counters involved. Wither has no interaction with this portion of the damage at all.

Example: You attack with a 5/5 creature with wither and trample. Your opponent blocks with a 2/2. You assign 2 damage to the blocker (it gets two -1/-1 counters and dies) and 3 trample damage to your opponent. Your opponent simply loses 3 life — no -1/-1 counters are placed anywhere.

So wither and trample interact cleanly: wither affects only the damage assigned to blocking creatures, while trample damage hitting a player behaves as ordinary combat damage.