Alphabet as a whole yes, but the question I think is how much they made from Google Shopping specifically. If the fine was greater than amount of money they made with what they were getting fined about (multiplied by the chance of getting caught, probably higher for google than most), then they EU would successfully discourage similar rule breaking in the future. While alphabet's total income for the year may be that high, most of that comes from ads and not shopping, and penalizing just the shopping related income makes sense in that light.

The alternative argument is that what you really want a fine to do is penalize law-infringing heavily enough that a companies' shareholders make not getting fined again high priority. In that light, you're primarily concerned about levying fines against a company's profit margin/funds they're using to invest in future growth. In which case, yeah, this fine is far too paltry to concern investors in a vacuum.