Yes. This is especially true if you took all your gen ed. classes in the first two years - they care more about the courses you took in your major, which are usually courses you take from sophomore year onward. Some schools (like Berkeley I think) ask you to actually calculate your GPA from the past two years. If you really blew it freshman year, you might include an addendum where you discuss the reasons why: it would be appropriate to mention there what your GPA would be if you excluded your courses from freshman year, or the courses you took when you were in a different major, etc.
Furthermore, if you're in a master's program, your grades from the master's program matter more than from undergrad.