I think they were referring to net contributions - Malta is a massive net recipient per capita (https://inews.co.uk/explainers/charts/much-uk-pays-eu-much-g...)
What happens with those paid fees is complex, but agreed between the members. Roughly described:
* the fees go to the EU budget
* some of the fees are used to pay for EU administration
* some of the fees are used to pay for EU projects
* one big program is "Investment in depressed regions, EU-wide". The UK is not a big beneficiary of this program because fortunately its regions are relatively rich. Some regions are poor, and they do receive funds.
The reason why the UK is net contributor is because it is a rich country.
Its gross contribution is small, GDP and capita-wise.