In a "normal" situation in the last couple of centuries in the UK, the governing party would have a large majority, and would be in a position to win most meaningful votes in parliament fairly easily. That would make whipped abstentions for any section of the party relatively rare. Members of the government (including ministers not in the cabinet) would be expected never to vote against the government position where it had one, so only being at liberty to choose how to vote on true free votes on matters of conscience.
However, we are not in a normal situation. In particular the May administration has on occasion ordered the entire party (not just the cabinet) to abstain in motions on "opposition days" (when the business of the day has been chosen by the two largest opposition parties, i.e. the Labour party and SNP). This is generally understood to have been to prevent losing anyway due to individual backbench rebellions on relatively trivial votes.
In terms of penalties, Ministers serve at the pleasure of the Prime Minister, so a cabinet member who wanted to vote anyway could resign, or expect to be sacked. Disobeying will also affect the MPs standing within the party hierarchy, but given how divided both major parties have been on Brexit, this may not be as important as it might be otherwise, especially since Mrs May is now widely seen as a "lame duck" Prime Minister.
It's worth noting that although this is presented as ordering the cabinet to abstain, it could also be seen as allowing more junior ministers to vote, despite the fact that the continuing Government position that accepting the draft Withdrawal agreement is the only feasible option.