Samus has a super hard time against rushdown and projectile users. Anyone who can pester her from charging or even approaching is a hard time, and fast characters who dont let her escape are as well. My personal experience - I feel like I hit a wall against some characters (and also some aggressive or disruptive playstyles). Switching out from Samus to a different fighter has helped in each case.
Maybe you're trying to hard to charge your beam?
Don't underestimate the usefulness of partially charged
shots. They come out faster than missiles and can
still do respectable damage.
Samus basically has to make her own opportunities to charge.
Contrary to what you many may think is the sound course
of action, it may be more beneficial for Samus to start
fighting in close quarters (albeit with some caution of course).
Using her various pokes (Zair, Ftilt and Dtilt) and most importantly,
morph ball feints to keep her relatively safe (And don't forget
short-hopped Uairs!). Now, it's important to remain unpredictable
with your bombs, since you can get hit rather easily if
they predict your movement (the bomb helps a bit but shouldn't
be relied on heavily).
Once you start knocking them relatively far, then you can charge
your beam more safely. Basically, if you try charging your
beam while your opponent isn't indisposed in any way, you're
more likely to be disrupted.
This was more for the rushdown characters. I got
nothing other projectile users, other than maybe stay mobile
and wait for chances. You can maybe throw off people
trying to catch your landings with down b.