The taxpayer is ultimately responsible, but many reputable CPA's will reimburse you for any penalties you incur because of their honest mistake.
If you are assessed penalties through no fault of your own, you can also request abatement by filing IRS Form 843: https://www.irs.gov/pub/irs-pdf/f843.pdf
Note that a separate 843 is needed for each tax year involved.
**Answers are correct to the best of my ability but do not constitute tax or legal advice.
