When starting out with your first colony...
Build an orbital station as soon as possible, ideally after Spaceport
If major factions do not send expeditions at you, pirates will be sent instead, and they come fairly early. Their raids are not as powerful as expeditions from major factions, but you need the station to have a chance to defeat their raids without your direct intervention. If you need a waystation before the orbital station, that is fine (you want to be able to restock on crew, supplies, and fuel), but you probably need to defend against that first raid personally.
Build Patrol HQ early
You need a patrol or two to reclaim relays that got stolen periodically by enemies. This does not need to be built immediately, but it is annoying going back yourself to reclaim relays and your stability.
Do NOT use Free Port early
1) It aggravates Luddic Church and Hegemony to send expeditions at you. They do not send expeditions if you do not have Free Port on. That leaves Diktat, League, and Tri-Tachyon sending expeditions at you for producing too much, if pirates do not raid.
2) It makes expeditions more frequent.
3) It lowers stability, which you probably have not stacked up high.
4) It does not increase income enough until you start producing organs (at size 6) and you can maintain 10 stability even with -3 penalty. Free Port is very useful for population growth too, but until you can defend against expeditions, colony growing faster than your fleet or capability to deal with is not a good idea.
Do NOT use Growth Incentives early
Growing colony fast sounds nice, until that expedition you cannot deal with because you could not build up or upgrade your fleet and colony defenses fast enough wrecks everything. Colony growth increases production, which is the last thing you want when trying to keep a low enough profile to avoid their attention. Once you can deal with expeditions, then crank it as high as you can afford, but not before then.
Do NOT use industries that produce too much of a given commodity
Any amount from Fuel Production or Heavy Industry will aggravate Diktat or League. I think Light Industry might aggravate early as well. The only safe industries early that can produce stuff for money are Farming, Tech Mining (via loot), and maybe Mining. Mining will aggravate Tri-Tachyon if too much (rare) ore is produced. Stuff like ultrarich ores, Industrial Planning, or colony growth can put ore production over the top. By size 5, your colony might be too big to limit production enough, and you need to be ready to deal with expeditions. Once you decide you are ready enough for expeditions, then get Industrial Planning and build Heavy Industry and those other vital jackpot industries.
Do NOT take Industrial Planning 2 early
The perk that increases production commodities by one, which is useful for meeting demand and increasing profits, might make you produce too much stuff (see above) and attract expeditions. Use administrators for Industrial Planning if you must, but do not get the skill yourself until you are ready to deal with expeditions from majors.
Pather Cells are bugged and are mostly harmless
As long as colony stability is 2 or higher, all attempts at sabotage will fail. The worst they can do is a permanent -1 stability if you do not seek out and destroy Pather bases. This will be fixed next release, but that is months or longer down the line.