I had same problem on my CX-5 thought it was suspension or strut issue. It really bugged me going over bump roads, speed bumps, etc. I found this TSB and dealer performed the service and problem has been corrected. Mine turned out to be the A-pillar listed below. All is quiet now.
TSB 09-009/12
APPLICABLE MODEL(S)/VINS
2013 CX-5 vehicles with VINs lower than JM3KE******128359 (produced on or before June 1, 2012)
DESCRIPTION
While driving over rough or bumpy roads, some vehicles may exhibit a rattle noise from the instrument panel and/or a creak noise from the A-pillar.
Rattle Noise From Instrument Panel:
This noise may be caused by low cowl panel mounting bolt torque. The bolt torque control and inspection has been improved during the mass-production of vehicles with VINs JM3KE******107376 (produced February 10, 2012) or higher.
Creak Noise From A-Pillar:
This noise may be caused by two joined panels scraping together at the A-pillar. The panel weld areas have been improved during the mass-production of vehicles with VINs JM3KE******128359 (produced June 1, 2012) or higher.