Yes, it affects your tax return.
It's a benefit of employment so it might be taxable, for one. If so, DND should be issuing you your T4 with a notation (one of the boxes) that includes the benefit of employment.
It's not a bursary/scholarship which are treated differently for tax purposes (they're not taxed, but benefits of employment generally are).
If there's nothing on your T4 as a benefit of employment then you should be deducting the amount you received from the CF from the amount you tell the tax man that you paid for education. This is because you shouldn't be allowed to claim a tax credit for an amount YOU didn't actually pay.
It's a bit confusing because when you get issued your T2202A or whateverthenumber it just says the amount you paid for tuition...not who paid it. And if on the T4 it doesn't include the benefit, and DND doesn't issue you anything else (they really should but I don't know what number it would be) then how are you really supposed to know what to do?
Sadly the CRA isn't at all tolerant of ignorance in failure to properly file your taxes, so.... if in doubt, contact the education reimbursement coordinator. I think the Pacific region one is Helen Bates at CFB Naden. She's very helpful.
WWPD