They don't count for a lot because a lot of practicing doctors don't use the type of material you're taught first year and don't particurally like it. This has become even more true in recent years where the amount of biochemistry, molecular/cellular biology, and genetics has skyrocketted. So if you don't do stupendously first year, it won't kill you.
However, it will hurt you if you fail a lot of classes. Even though it's not the most relevant stuff, if you can't manage to pass that reflects poorly on your mental abilities or your dedication to the field, or both.
That being said, you'll have to take Step 1 after second year and you'll have a decent amount of that material on that examination (especially in the areas I said above that aren't clinically relevant) so might as well learn it well the first time.
Also, depending on your school, even if your school doesn't have a "GPA", a lot of schools secretely tabulate class ranks. Some of them only use them for AOA purposes, some of them actually put it on your Dean's letter. The rumor around my school is that even though the administration claim they don't keep track of class rank for anything but awards and AOA, they DO put it on your Dean's letter.