If you're comparing to a beer produced in a brewery, it could be difference in types of hop used and freshness. Are you using whole hops or are you using pellets? Most homebrewers I know (myself included) use the hop pellets you get at your LHBS because they're the most available.
I could be wrong on this, but my understanding of hops besides whether they introduce bitterness or aroma into your beer, is independent on the type of malts or yeasts you use. The only thing I can think of that might affect hops and the flavour of your resulting beer is your water profile (tap water, bottled, filtered, etc) and its pH level.
Have you tried experimenting with the amount of hops you're using? If you're finding the hops are too strong, try reducing the amount. A general rule of thumb if you're using a new hop is to add in about 1-2 oz (28-56g) to a five gallon batch (19L) and work your way up or down from there.