I don't see Bayer Leverkusen having any difficulty getting into the semifinals now, in fact they have still managed to maintain an unbeatable record throughout this season in all competitions.
We must not only look at a few matches, but we must measure the overall strength of the team from the matches they play.
Roma is indeed a strong team, they have made quite positive progress since being handled by De Rossi and indeed the possibility of Roma being able to beat Bayern Leverkusen as you said is still there, especially in the Europa League semifinal match, the team will definitely give their best performance.
However, I look at this realistically and the percentage of Roma being able to beat Bayern Leverkusen is quite small, Bayern Leverkusen has everything better than Roma so I think there will be no surprises, Bayern Leverkusen is still the team that is the favorite this season to win the title .
At the moment, the UEL this season is left with 4 teams set to battle it all out at the semi finals. The strongest team said to be Leverkusen will be facing the second toughest Roma and I must say it all seems like the UEFA board wants Leverkusen to go home with the trophy. Comparing the probability of the game outcome taking into consideration both teams performances so far, Leverkusen is the better side and they have the greater advantage over Roma. Yes Roma can be competitive and can make the game tough but Leverkusen's record won't let them stay down to be defeated. Really it'll be a game to look out for as in the first and second legs, both teams would put up their best to seeing if they can secure the 3points.
The last two teams aren't much of big strengths as they've had minor records so far in their European cup quests. If either of them wins, it'll be a walkover game for their final opponent because either Roma or Leverkusen would be a better side to them considering experiences gained and domestic league performances this season. Atalanta or Marseille aren't tough teams and if I'm to predict the qualified team to be, I'd go for Atalanta based on they are a little above the average performance of their normal performance. The semi finals won't be an easy battle as anything really can happen on the field of play.
Leverkusen's qualification to the semi finals of this season's UEL was also historic as they kept their unbeaten record still in play after drawing to West ham. This season they've been an undaunted team and they really have all it takes to finish the season with the unbeaten record intact and two trophies in their shelf. Their next UEL opponent is competitive but it's not really a big deal for them based on the fact that they have gained enough confidence and have even being in tougher encounters which they've at thesame time comfortably come out from victoriously. Roma themselves know that they won't be up for a joke game in the semi finals stage.