If your horse really objects to having his mane backcombed, you could use a tail rake on the underside to gradually thin it. Alternatively, use scissors to cut up at an angle, taking care not to snip too much at a time.
Try not to comb your horse’s mane and tail through when it’s dirty without using a conditioner or mane and tail spray. Tugging through the hair will damage it, potentially leaving you with a scraggly look.