Why are you under the impression that putting it in a tube makes handling turbing forces, stopping forces and control more difficult? Inside a tube, all motion is perfectly constrained, and you have a tremendous amount of surface area to magnetic brake against.
The turning radii issues are of course real, and are highly addressed in the Hyperloop Alpha document. Likewise for dimensional precision. For smoothness, their solution is a radial polisher which drives down the tube behind the pipelaying crew and smoothing out each orbital weld (and the pipe itself). For straightness, alignment is maintained by the same suspension/alignment system they use to deal with earthquakes.
As for why maglev trains are expensive - trains are expensive for a wide variety of reasons. Land acquisition and permitting is often the most expensive. Tunnels and viaducts are often a very large component as well. Maglev technology itself often tends to have high bills.
Hyperloop (as per Hyperloop Alpha, not the student competition) isn't maglev, it's an air bearing system. Skis, basically. The pipe is built the same as oil pipeline, and the budget is similar to that of oil pipeline budgeting per unit area per unit distance (oil pipelines have harder environmental issues to overcome and much higher loadings, more significant temperature management issues, etc, but lower precision / straightness requirements, so it's probably a wash). Tunnel cost is minimized by minimizing tube size (the budgeted tunnels are standard rates for tunneled pipe in non-urban areas). Viaduct costs are minimized by a key design feature of Hyperloop - minimizing peak loadings by having frequent, small vehicle launches rather than infrequent, large vehicle launches. Viaduct costs tend to track their peak loading.
As for land acquisition, the costs in Hyperloop Alpha are kept down by a combination of design and cheating. As per design, it's designed to be small enough to fit elevated into highway medians, with the low peak loadings, making overhead suspension an affordable option. Such places are state land, and already permitted for far more environmentally harmful activity (road traffic). This of course requires state buy-in to the concept, but states often specifically pursue high speed transport options. Private land acquisition is limited to places needed to maximize turning radii, and in-city for stations. The latter is the other place that they cheat - Hyperloop Alpha avoids cities. LA and San Francisco are served by it, according to the design, like airports on the outskirts of town; people have to get connecting legs into town. But that would be an unpopular decision, and you would expect the state to insist on greater accessibility (airports are only out of town because they have to be, not because that's a desirable location). Likewise it bypasses cities en route, unlike HSR. Basically, it's designed as something halfway in-between HSR and air travel (both in terms of service and throughput), but targeting much lower prices, higher speeds, and a lower energy footprint.
In short, it's budget savings vs. HSR are somewhat of a combination of cheating (cutting out a lot of what HSR does) and design (keeping track loadings down, profile small, build in the same manner as an established industry (pipeline), and moving your hardware (capital expense) through the system as quickly as you can.