Assuming you mean ministers not ministries (a separate Department for Trams seems completely implausible, so I'm assuming that's a typo), it's worth noting that there are limits on the numbers of paid ministers the Government is allowed to have at once.* Currently the total maximum number is 109, but within this there are maximum numbers for Cabinet ministers, ministers of state, other ministers, whips etc. This is for a very good reason - it wouldn't be healthy for the governing party or coalition to have too many of its MPs as part of the 'payroll vote', limiting opportunities for internal dissent and scrutiny. In addition, it needs MPs to carry out various non-ministerial roles (parliamentary private secretaries, select committee members and chairs etc.), plus there will always be a number of MPs who either do not want to be a minister or who are thought to be unsuitable for one reason or another. All this means that the Government can't appoint as many ministers as it wants - if it wants more in one department, it has to reduce them in another.
The DfT currently has has six ministers. Active travel is currently one of Trudy Harrison's ten listed responsibilities, while buses and light rail are two of Baroness Vere's five listed responsibilities. Giving each of those three areas its own minister without changing anything else in the DfT would mean it'd have nine ministers, and there'd be three less ministers elsewhere in the Government.* This would give the DfT the most ministers of any department other than the Cabinet Office, alongside the Foreign Office and Home Office (and as both those departments have ministers whose role is partially in other departments, it would arguably make DfT the second overall). Realistically, that's completely unjustifiable - yes, transport is important; no, it's not that important.
Obviously, you can reprioritise things while keeping the same number of ministers by rearranging their responsibilities, but there may be other factors constraining this (e.g. the amount of legislation and other work expected for different policy areas). Ultimately, like a lot of Government, it's about making choices and picking priorities as you very rarely have the resources or ability to do absolutely everything you want. If you want to spend more time on one thing, chances are something else will have to give, either in that department or elsewhere.
*Though there is no limit on the number of unpaid ministers.
I think CH-H has got the tougher job. I wonder who told Boris they wanted things moved around.
