Yes, the bonus applies to workers and colonists as well as explorers and "traditional" military units.
I loaded up a late-game save and checked with a newly settled city that had relatively low production. The game speed was quick, so the numbers might not align with your numbers if you play at a different speed.
No Repair Facility:
- Colonist: 15 turns (124 production at 8.8/turn)
- Worker: 6 turns (40 production at 7.8/turn)
- Explorer: 4 turns (26 production at 7.8/turn)
- Aegis: 13 turns (120 production at 9.3/turn)
(I have some bonus military production abilities, which is why I get additional production per turn for the Aegis that you don't see otherwise. Also note that the Colonist gets bonus production because the city rebalances citizens when you pick it)
I then purchased a Repair Facility in that city.
With Repair Facility:
- Colonist: 14 turns (124 production at 9.4/turn)
- Worker: 5 turns (40 production at 8.4/turn)
- Explorer: 4 turns (26 production at 8.4/turn)
- Aegis: 13 turns (120 production at 9.9/turn)
As you can see, adding the Repair Facility boosted the production rate of both the military units and the non-military units. It didn't seem to be 10% for me, but it's possible that it's 10% of the base production and other modifiers were already applied in my first set of numbers. Regardless, there was an improvement in production from the Repair Facility.