1) We're building our full size airship to fly at 60 mph, which increases the usability in inclement weather.
2) Joe answered this in another comment, but our airships use pretty small quantities of helium compared to the bigger ones, so it's not a major operational cost.
3) For sure this is an issue, but the bigger the blimp is, the more bullet holes you'd have to fill it with to prevent it from reaching its final destination. The german zeppelins of world war I were really hard to shoot down. See 5:47 of the below video.
And hey I'm just spit-balling here but isn't wind a much less of an issue at dusk, night, and dawn? Would this not be a significant factor in when you would operate? I would imagine most people shooting 747s on passing trains aren't getting out of bed to do that, after all.
Or maybe paint them as sharks, then add some powerful lasers on their back:)
1) Weather. Moving at 35 mph it seems that a lot of long term planning is in order for something that could be severely impacted by weather. This sounds like a logistical nightmare during a week of active weather across the country.
2) Helium availability - there have been reports that the costs of helium have gone up considerably since there are only a very few producers of the gas and this seems like it would be a huge consumer of such gas.
3) Vandalism. Never underestimate the power of stupid people. It's well known in the railroad industry that trains and their cargo often take bullets from traveling cross country. In fact, the 737 fuselages that travel across country on trains for Boeing often have bullet holes in them that must be repaired. Add in a huge cargo blimp that is unmanned and the urge for vandalism will be significant for some nefarious actors.