Any new colony on an earth-like planet will have all three - sea, air, and land.
On Earth, water-based shipping is slow but cheap. Natural ports and harbors allow for transportation across oceans and seas and along rivers with ease. Water is still necessary for human life, so settlements will still be built along rivers.
As soon as there are multiple colonies located across large bodies of water that wish to trade, seaports will be the immediate and logical solution.
Air travel is great - you can carry people and goods across long distances without worrying about natural barriers. However, it's an energy guzzler and has limited capacity. In addition, it requires dedicated infrastructure, requires high demand to function economically (e.g. fly-over territory with low demand exists), etc.
There is no doubt that air travel will be used in any new colony. But there will need to be sufficient inter-city demand to justify the enormous capital expenditure necessary to build the infrastructure and vehicles.
First thing's first - HyperLoop and MagLev are not going to outright replace rail, even if starting from scratch. The technology is expensive, the capital costs are expensive, and both require complete grade separation to work.
HyperLoop: The benefit of HyperLoop is speed, which means that it is good for people but not for freight. Higher speeds require blasting holes in mountains and elevating the system above ground to maintain consistent height and avoid ground conditions. Keeping the entire system in a vacuum requires energy and results in high maintenance costs. Capital costs are high, and it is only relevant for medium-long distance land travel.
MagLev: The main advantage of MagLevs, like HyperLoop, involves their ability to reduce maintenance costs and increase speed by not having the vehicle touch the track. Again, capital costs are high, and they are unsuited for freight. Even low speed MagLevs can be economically unfeasible - The Linimo is famous for not running during high winds and for not running when there were too many passengers for it to actually levitate. In addition, their switches consists of many moving parts. They have their place, but they have their disadvantages as well.
Rail: Conventional rail is comparatively low tech and cheap material-wise to install. It's easy to set up, and is very flexible. However, on a new colony rail would most likely be for freight. Long, heavy trains going long distances are very good economically. As for long distance passenger service, I see other modes being preferred - if you're starting from scratch, you can choose your standard, and economies of scale will do the rest.
Roads: Roads are cheap and flexible. They will almost always exist in some form, even for longer distances. There will always be materials that cannot be transported by other means, and as such roads will be necessary to transport them. I don't see people using roads for long distance travel, but they will almost certainly exist.