There are of course many ways to do this (attach a truss (1D elements) to a cylinder (2D elements)
1) how finely meshed is the cylinder ?
2) how are you attaching them in the real world ? I suspect a lug with a bolt, or some such.
The easiest way is to project the truss element onto the shell and have a common node. A key to this is also respecting the real world attachment freedoms/stiffnesses. If you've modelled the truss with beam elements and the shell with plates, then you will need to release some of the bending freedoms (that don't exist in the real world). But this will, as I think you've already done, give you high localised stresses. To which you say "these stresses are not real, they are an artifice of the FEM" and do a hand calc (to pass the truss load across the bolt, into the lug, and from the lug into the shell (locally). But then this sounds like "I tried to use a mpc pin connection between the endpoints of the truss unit and a bit of the shell unit, but this results in a large stress concentration, which is not what I want", so maybe you've done this without resolving the fictitious high stresses ?
If you large large elements in the shell, you can do mesh refinement at the connections, to localise the high stresses to something within your lug.
And this leads to the next idea. Model the lug. I don't like this approach, I see it as a waste of computer resources (and one day the machines will rise up and extract a price for this). I see this as an extension of the common belief that FEMs are Right, and a reluctance to say "I can solve this problem with math".
Another thing you can do is to use a stiffness element (NASTRAN have CBUSH elements, I'm sure ABAQUS has something similar) to add an artificial stiffness/flexibility between the truss and the shell
"Hoffen wir mal, dass alles gut geht !"
General Paulus, Nov 1942, outside Stalingrad after the launch of Operation Uranus.