You say they lose like it's a common occurence. Like they don't every advantage except numbers on their side. And in the relatively cramped corridors of a starship, the weight of numbers can't truly be brought to bear against them in the ways that count. Do you seriously think a single company of Space Marines couldn't board and take a battleship or grand cruiser? They're only outnumbered about 1,000 to 1, that's not enough.

And even with all the limitations imposed upon their naval assets, they have some of the most advanced ships in space, the Mechanicus certainly hold back too much with the tech when it comes to the Astartes. Their general strategy tends toward fast, heavily armoured ships, with close range weaponry that facilitates boarding actions, and of course planetary assault. And for all the limitations, pretty much everyone knows their bucking them and have naval assets in excess of what everyone else would prefer they have (but just what the hell are they going to do about it?).

You should recheck the armaments of Light Cruisers too, they're not more heavily armed than a Strike Cruiser, the bombardment cannon alone is more than anything most Light Cruisers carry.

And of course a Grand Cruiser is the equal of a battlebarge, it's in the same weight class as battleships too.

Blood Pact said:

^^^ This!
Space marines are the first and last word when it comes to boarding actions and swift, decisive battles. Although the situation wherein astartes would be reclaiming illegally held land raiders is far from a common occurrence, i consider it pretty obvious how it would play out:

The rogue trader will find their ship (or fleet of small vessels, such as raiders, frigates and light cruisers) under attack suddenly from heavily armour escorts - think lots of close range batteries and lance fire. The Astartes escorts will help punch a hole for the strike cruiser to barrel its way  into the rogue trader's flagship. At this point they will launch swarms of thunderhawks and boarding torpedos.

Nothing short of a wall of strike craft and flak, or just running away, will save the rogue trader from having their flagship boarded and once on board the Astartes will mulch their way through the armsmen, no matter how well armed. In fact you'd need to be equipping your armsmen with heavy carapace or power armour and will bolt, plasma or melta weaponry to even stand a chance - flak armour and lasguns and shotguns will do nothing.

Once the boarding has commenced, the Astartes escorts will pull back while providing withering covering fire for the strike cruiser to pummel the enemy fleet with its close in batteries and bombardment cannons, so unless the rogue trader happens to have a fleet of multiple cruisers outfitted for war all in the same area at the same time, and has enough escorts to keep them from being flanked then they are going take crippling damage. And IF they happened to have that big a fleet then i guess the Astartes would have considered the rogue trader a far bigger threat and likely sent a battle barge and/or multiple strike cruisers. Oh and they could always be owed some favours by the Inquisition, who can always just get Officio Assassins on board the rogue trader vessels and start taking out command officers and threatening the stability of the fleet.

There really is little a rogue trader can do if they piss off the upper echelons of the Imperium other than hiding outside the Imperium at which point they kind of lose out on the whole point of being a rogue trader - the ability to trade between the Imperium and the outside galaxy for massive profit, whilst having the resources of the Imperium at their disposal (pending payment, of course).

While a minor Rogue Trader is not of a match for a Marine Chapter a powerful Dynasty can be more than a match. At least more than they are probably willing to risk.
I'm not saying they won't be able to defeat them I say they would rather try diplomatic channels before engaging combat, especially against someone also serving the Imperium.

A large Rogue Trader Dynasty can have dozens if not more ships including Grand Cruisers and Battle Cruisers. Engaging them in space combat will cause utter devastation on both sides. 

Space Marines are cool and awesome, they are not stupid. They will not fight a powerful rogue trader unless they have no other choice. And while the bolter is a powerful weapon, sometimes diplomacy is better.