Is the not arming civilian policy stupid or....?

I don't think it is a flaw in logic at all.

Much like planes, there are vastly more civilian/corporate unarmed spaceships than military/paramilitary/security armed spaceships. Unarmed ships getting attacked is likely a rare occurrence; Shepard just seemingly ends up having to deal with a few of them in the trilogy.

P.S. Thermal clips are better.

i mean they were able to arm an entire fleet in a short amount of time. 

It's a definite flaw in the universe.

Such things as going to a whole other galaxy, with zero armament on either your ships or the space station intended to house a large portion of your population, is a lesson in stupidity given the established nature of the setting.

Yes, that was stupid. Also I felt the ambassador discussion where you stop the angaran diplomatic guards from being armed was stupid. You should have been given the option to agree with them. Allowing armed guards for diplomats who aren’t yet sure of your nature seems a no brainer.

we don't arm civilian cruises or cargo ships. Not sure why it should be different because of them being "Space Cruise Ships" and "Space Cargo Ships". Do we really want civilian ships armed and potentially able to band together to become a threat?

As far as Tempest, I generally agree. It should have had some weapons. I thought the idea was that it was faster without weapons but going into the unknown is reason enough. Or, even if the Tempest itself had no weapons, it should have had an armed escort. That said, the plan was to have the Nexus as a hub while multiple planets were colonized. Then they'd build their armed ships. That plan all went to hell.

 Planes and space ships are two different creatures.  In space it is far closer to modern day ships which piracy is a problem due to vessels being attacked. They even made a movie with Tom Hanks about it.

....the whole arming the civilian ship is just a terrible and dumb idea. It only take someone with bigger gun to kill you.

As in case on Rannoch, arming the civilian ship only get them being seen as a threat and shot down. As Joker said, you don't put guns on school busses.

I'd say it depends. The problem with the Mass Effect Universe is that the environment is not really that consistent.

In Mass Effect 1, the universe feels much less explored, even council space (and especially the Attican Traverse) seems to have much less infrastructure than in ME2/3. Therefore, I'd say the scenario in ME1 reminds me much more of the wild west or the high seas in the 18th/19th century. There even merchant vessels were fairly heavily armed and civilian transports had armed personal. The reason of course is that they had to rely on themselves for protection while traversing much longer distances (in terms of time away from the nearest outpost/harbor) on their own and they couldn't call for help quickly or easily. In that scenario, for every vessel to have at least some rudimentary armament makes sense.
The reaper invasion changes all that of course, as we have seen.

For the Andromeda expedition basically not to be armed at all was of course a bit of a stupid idea but IMO, that was very much consistent with the general stupidity of that expedition as a whole. I applaud the writers for keeping their stupidity at maximum level at all times.

I think there's a difference between allowing citizens to bear arms and arming cargo ships that become targets due to having weapons.  Ask the quarians about it.

Some good the "no weapons = no threat" philosophy did for the Initiative when they encountered the Khett in Andromeda. In fact, the reason why the Khett were such a problem is specifically because the Initiative lacked the capacity to fight back in any way except on foot.

Indeed, there is even a side mission to locate missing shuttles that touches upon this point perfectly. Because the settlers' ships and transports lacked any sort of defensive armament the Khett actually increased their pursuit of refugees when they would flee the colonies. It was only after one shuttle weaponized it's drive core, destroying the pursuing Khett ships, that the attacks stopped.

I'm sorry but the whole, "don't arm civilian vessels because it makes them a target" makes no sense. If I'm a pirate/slaver/kett/whatever I'm going after the civilians who can't fire back, not the ones who can.

I love Andromeda but I see both sides of it. However some weapons should have been on the ship, but at the same time wouldn't have given the best first impression.