Question: My guidance counselor didn't tell me about the CSS Profile form so I did not hand it in by the deadline. If I send it in about a week and a half late, are they going to accept it and is it going to count against me?
Ultimately it is YOU and not your guidance counselor who needs to stay on top of college requirements and deadlines. Colleges post this information on their Web sites and it's your responsibility to see what you must submit. Guidance counselors can't possibly keep track of all of their students' target colleges and their differing demands.
BUT ... admission and financial aid officials do realize that this is a crazy and confusing process, so it's likely that they will cut you a little slack despite the tardy Profile. Submit the form ASAP and then send a brief email note to the financial aid office at every college where its overdue. Explain the oversight. If your parents didn't attend college or if your counselor has a giant case load and doesn't have time to provide adequate assistance to every student, it's fine to say that, too. (You should be able to find the appropriate email address on the college's financial aid Web pages. It's okay to write to the admission office instead, as well.)
Note that many colleges do not require the CSS Profile, but some schools do have their own forms that must be submitted in addition to the FAFSA. So read all Web site instructions and checklists carefully to make sure that you're not missing anything else.