Dawnguard are in the grand scheme of things the good guys and the Vampires are the bad guys to the people of Skyrim.
Though once you get to know them you find out they are all cold hearted monsters more willing to kill than the Vampires and they want to kill the Vampires because they are doing what they have to, to survive which is drink the blood of humanoid beings.
The Vampires at first glance seem awfully evil but some of them are genuinely nice..such as Serana then again she has an evil side..if you are a human she starts flirting and tempting your character into becoming a vampire because she loves the dragonborn...and his/her blood and wants to spend eternity with him/her.
Pretty much how I look at it..
The Dawnguard want to kill an entire race of beings because they are doing what comes naturally to them.