Uhh, yeah. That's what entertainment largely is. It's not limited to relationships (that go both way, btw, since the same concept also exists for girls in the traditional shoujo, where both the princes on white and black horses just happen to choose the ordinary girl (figuratively speaking)). It's the same thing about all kinds of successes. In Utawarerumono the dude not only got the attention of the girls, he rose to a position of leadership, became a strong warrior, decided the fate of the nations, and whatnot, despite being nothing but a masked nobody in the beginning. Girls are just a single detail of many, so don't get stuck on it. You'll soon find yourself watching only... Dunno, slice of life or something, if anything unrealistic in fiction rubs you the wrong way.
That being said, I don't like harem either, when it clearly claims the center stage. I didn't really feel like that watching Utawarerumono back then.